diff --git a/apps/electron/package.json b/apps/electron/package.json
index 3d53211bfb..f0b9e6406d 100644
--- a/apps/electron/package.json
+++ b/apps/electron/package.json
@@ -24,6 +24,7 @@
   "main": "./dist/main.js",
   "devDependencies": {
     "@affine-test/kit": "workspace:*",
+    "@affine/env": "workspace:*",
     "@affine/native": "workspace:*",
     "@blocksuite/blocks": "0.0.0-20230705162600-2cb608e4-nightly",
     "@blocksuite/editor": "0.0.0-20230705162600-2cb608e4-nightly",
diff --git a/apps/electron/scripts/common.mjs b/apps/electron/scripts/common.mjs
index f3005cc308..3a0747c2b2 100644
--- a/apps/electron/scripts/common.mjs
+++ b/apps/electron/scripts/common.mjs
@@ -38,7 +38,12 @@ export const config = () => {
       bundle: true,
       target: `node${NODE_MAJOR_VERSION}`,
       platform: 'node',
-      external: ['electron', 'electron-updater', '@toeverything/plugin-infra'],
+      external: [
+        'electron',
+        'electron-updater',
+        '@toeverything/plugin-infra',
+        'yjs',
+      ],
       define: define,
       format: 'cjs',
       loader: {
diff --git a/apps/electron/src/helper/db/__tests__/migration.spec.ts b/apps/electron/src/helper/db/__tests__/migration.spec.ts
new file mode 100644
index 0000000000..06bf760c82
--- /dev/null
+++ b/apps/electron/src/helper/db/__tests__/migration.spec.ts
@@ -0,0 +1,69 @@
+import path from 'node:path';
+
+import { SqliteConnection } from '@affine/native';
+import { afterEach, describe, expect, it, vi } from 'vitest';
+import * as Y from 'yjs';
+
+import { removeWithRetry } from '../../../../tests/utils';
+import { copyToTemp, migrateToSubdocAndReplaceDatabase } from '../migration';
+
+const tmpDir = path.join(__dirname, 'tmp');
+const testDBFilePath = path.resolve(__dirname, 'old-db.affine');
+
+const appDataPath = path.join(tmpDir, 'app-data');
+
+vi.mock('../../main-rpc', () => ({
+  mainRPC: {
+    getPath: async () => appDataPath,
+  },
+}));
+
+afterEach(async () => {
+  await removeWithRetry(tmpDir);
+});
+
+describe('migrateToSubdocAndReplaceDatabase', () => {
+  it('should migrate and replace the database', async () => {
+    const copiedDbFilePath = await copyToTemp(testDBFilePath);
+    await migrateToSubdocAndReplaceDatabase(copiedDbFilePath);
+
+    const db = new SqliteConnection(copiedDbFilePath);
+    await db.connect();
+
+    // check if db has two rows, one for root doc and one for subdoc
+    const rows = await db.getAllUpdates();
+    expect(rows.length).toBe(2);
+
+    const rootUpdate = rows.find(row => row.docId === undefined)!.data;
+    const subdocUpdate = rows.find(row => row.docId !== undefined)!.data;
+
+    expect(rootUpdate).toBeDefined();
+    expect(subdocUpdate).toBeDefined();
+
+    // apply updates
+    const rootDoc = new Y.Doc();
+    Y.applyUpdate(rootDoc, rootUpdate);
+
+    // check if root doc has one subdoc
+    expect(rootDoc.subdocs.size).toBe(1);
+
+    // populates subdoc
+    Y.applyUpdate(rootDoc.subdocs.values().next().value, subdocUpdate);
+
+    // check if root doc's meta is correct
+    const meta = rootDoc.getMap('meta').toJSON();
+    expect(meta.workspaceVersion).toBe(1);
+    expect(meta.name).toBe('hiw');
+    expect(meta.pages.length).toBe(1);
+    const pageMeta = meta.pages[0];
+    expect(pageMeta.title).toBe('Welcome to AFFiNEd');
+
+    // get the subdoc through id
+    const subDoc = rootDoc
+      .getMap('spaces')
+      .get(`space:${pageMeta.id}`) as Y.Doc;
+    expect(subDoc).toEqual(rootDoc.subdocs.values().next().value);
+
+    await db.close();
+  });
+});
diff --git a/apps/electron/src/helper/db/__tests__/old-db.affine b/apps/electron/src/helper/db/__tests__/old-db.affine
new file mode 100644
index 0000000000..13906afe7a
Binary files /dev/null and b/apps/electron/src/helper/db/__tests__/old-db.affine differ
diff --git a/apps/electron/src/helper/db/migration.ts b/apps/electron/src/helper/db/migration.ts
new file mode 100644
index 0000000000..2d50b2c5f1
--- /dev/null
+++ b/apps/electron/src/helper/db/migration.ts
@@ -0,0 +1,55 @@
+import { resolve } from 'node:path';
+
+import { migrateToSubdoc } from '@affine/env/blocksuite';
+import { SqliteConnection } from '@affine/native';
+import fs from 'fs-extra';
+import { nanoid } from 'nanoid';
+import * as Y from 'yjs';
+
+import { mainRPC } from '../main-rpc';
+
+export const migrateToSubdocAndReplaceDatabase = async (path: string) => {
+  const db = new SqliteConnection(path);
+  await db.connect();
+
+  const rows = await db.getAllUpdates();
+  const originalDoc = new Y.Doc();
+
+  // 1. apply all updates to the root doc
+  rows.forEach(row => {
+    Y.applyUpdate(originalDoc, row.data);
+  });
+
+  // 2. migrate using migrateToSubdoc
+  const migratedDoc = migrateToSubdoc(originalDoc);
+
+  // 3. replace db rows with the migrated doc
+  await replaceRows(db, migratedDoc, true);
+
+  // 4. close db
+  await db.close();
+};
+
+export const copyToTemp = async (path: string) => {
+  const tmpDirPath = resolve(await mainRPC.getPath('sessionData'), 'tmp');
+  const tmpFilePath = resolve(tmpDirPath, nanoid());
+  await fs.ensureDir(tmpDirPath);
+  await fs.copyFile(path, tmpFilePath);
+  return tmpFilePath;
+};
+
+async function replaceRows(
+  db: SqliteConnection,
+  doc: Y.Doc,
+  isRoot: boolean
+): Promise<void> {
+  const migratedUpdates = Y.encodeStateAsUpdate(doc);
+  const docId = isRoot ? undefined : doc.guid;
+  const rows = [{ data: migratedUpdates, docId: docId }];
+  await db.replaceUpdates(docId, rows);
+  await Promise.all(
+    [...doc.subdocs].map(async subdoc => {
+      await replaceRows(db, subdoc, false);
+    })
+  );
+}
diff --git a/apps/electron/src/helper/dialog/dialog.ts b/apps/electron/src/helper/dialog/dialog.ts
index d58bd4a4a9..d9f9add1c9 100644
--- a/apps/electron/src/helper/dialog/dialog.ts
+++ b/apps/electron/src/helper/dialog/dialog.ts
@@ -1,9 +1,11 @@
 import path from 'node:path';
 
+import { ValidationResult } from '@affine/native';
 import fs from 'fs-extra';
 import { nanoid } from 'nanoid';
 
 import { ensureSQLiteDB } from '../db/ensure-db';
+import { copyToTemp, migrateToSubdocAndReplaceDatabase } from '../db/migration';
 import type { WorkspaceSQLiteDB } from '../db/workspace-db-adapter';
 import { logger } from '../logger';
 import { mainRPC } from '../main-rpc';
@@ -55,6 +57,7 @@ const ErrorMessages = [
   'DB_FILE_ALREADY_LOADED',
   'DB_FILE_PATH_INVALID',
   'DB_FILE_INVALID',
+  'DB_FILE_MIGRATION_FAILED',
   'FILE_ALREADY_EXISTS',
   'UNKNOWN_ERROR',
 ] as const;
@@ -191,27 +194,42 @@ export async function loadDBFile(): Promise<LoadDBFileResult> {
         ],
         message: 'Load Workspace from a AFFiNE file',
       }));
-    const filePath = ret.filePaths?.[0];
-    if (ret.canceled || !filePath) {
+    let originalPath = ret.filePaths?.[0];
+    if (ret.canceled || !originalPath) {
       logger.info('loadDBFile canceled');
       return { canceled: true };
     }
 
     // the imported file should not be in app data dir
-    if (filePath.startsWith(await getWorkspacesBasePath())) {
+    if (originalPath.startsWith(await getWorkspacesBasePath())) {
       logger.warn('loadDBFile: db file in app data dir');
       return { error: 'DB_FILE_PATH_INVALID' };
     }
 
-    if (await dbFileAlreadyLoaded(filePath)) {
+    if (await dbFileAlreadyLoaded(originalPath)) {
       logger.warn('loadDBFile: db file already loaded');
       return { error: 'DB_FILE_ALREADY_LOADED' };
     }
 
     const { SqliteConnection } = await import('@affine/native');
 
-    if (!(await SqliteConnection.validate(filePath))) {
-      // TODO: report invalid db file error?
+    const validationResult = await SqliteConnection.validate(originalPath);
+
+    if (validationResult === ValidationResult.MissingDocIdColumn) {
+      try {
+        const tmpDBPath = await copyToTemp(originalPath);
+        await migrateToSubdocAndReplaceDatabase(tmpDBPath);
+        originalPath = tmpDBPath;
+      } catch (error) {
+        logger.warn(`loadDBFile, migration failed: ${originalPath}`, error);
+        return { error: 'DB_FILE_MIGRATION_FAILED' };
+      }
+    }
+
+    if (
+      validationResult !== ValidationResult.MissingDocIdColumn &&
+      validationResult !== ValidationResult.Valid
+    ) {
       return { error: 'DB_FILE_INVALID' }; // invalid db file
     }
 
@@ -220,9 +238,8 @@ export async function loadDBFile(): Promise<LoadDBFileResult> {
     const internalFilePath = await getWorkspaceDBPath(workspaceId);
 
     await fs.ensureDir(await getWorkspacesBasePath());
-
-    await fs.copy(filePath, internalFilePath);
-    logger.info(`loadDBFile, copy: ${filePath} -> ${internalFilePath}`);
+    await fs.copy(originalPath, internalFilePath);
+    logger.info(`loadDBFile, copy: ${originalPath} -> ${internalFilePath}`);
 
     await storeWorkspaceMeta(workspaceId, {
       id: workspaceId,
diff --git a/apps/electron/tsconfig.json b/apps/electron/tsconfig.json
index fe899d5c2a..fabecbe665 100644
--- a/apps/electron/tsconfig.json
+++ b/apps/electron/tsconfig.json
@@ -25,6 +25,9 @@
     {
       "path": "../../packages/infra"
     },
+    {
+      "path": "../../packages/env"
+    },
 
     // Tests
     {
diff --git a/packages/i18n/src/resources/en.json b/packages/i18n/src/resources/en.json
index fef108c6a4..b3db8c6e7b 100644
--- a/packages/i18n/src/resources/en.json
+++ b/packages/i18n/src/resources/en.json
@@ -313,6 +313,7 @@
   "Move folder hint": "Select a new storage location.",
   "Storage Folder": "Storage Folder",
   "DB_FILE_INVALID": "Invalid Database file",
+  "DB_FILE_MIGRATION_FAILED": "Database file migration failed",
   "Name Your Workspace": "Name Your Workspace",
   "Change avatar hint": "New avatar will be shown for everyone.",
   "Change workspace name hint": "New name will be shown for everyone.",
diff --git a/packages/native/index.d.ts b/packages/native/index.d.ts
index 0d7140afdc..5c7f194f98 100644
--- a/packages/native/index.d.ts
+++ b/packages/native/index.d.ts
@@ -7,7 +7,7 @@ export interface WatchOptions {
   recursive?: boolean;
 }
 /** Watcher kind enumeration */
-export const enum WatcherKind {
+export enum WatcherKind {
   /** inotify backend (linux) */
   Inotify = 'Inotify',
   /** FS-Event backend (mac) */
@@ -38,6 +38,12 @@ export interface InsertRow {
   docId?: string;
   data: Uint8Array;
 }
+export enum ValidationResult {
+  MissingTables = 0,
+  MissingDocIdColumn = 1,
+  GeneralError = 2,
+  Valid = 3,
+}
 export class Subscription {
   toString(): string;
   unsubscribe(): void;
@@ -71,5 +77,6 @@ export class SqliteConnection {
   ): Promise<void>;
   close(): Promise<void>;
   get isClose(): boolean;
-  static validate(path: string): Promise<boolean>;
+  static validate(path: string): Promise<ValidationResult>;
+  migrateAddDocId(): Promise<void>;
 }
diff --git a/packages/native/index.js b/packages/native/index.js
index 98d9a450fe..f985c7ef0e 100644
--- a/packages/native/index.js
+++ b/packages/native/index.js
@@ -263,11 +263,18 @@ if (!nativeBinding) {
   throw new Error(`Failed to load native binding`);
 }
 
-const { WatcherKind, Subscription, FsWatcher, moveFile, SqliteConnection } =
-  nativeBinding;
+const {
+  WatcherKind,
+  Subscription,
+  FsWatcher,
+  moveFile,
+  SqliteConnection,
+  ValidationResult,
+} = nativeBinding;
 
 module.exports.WatcherKind = WatcherKind;
 module.exports.Subscription = Subscription;
 module.exports.FsWatcher = FsWatcher;
 module.exports.moveFile = moveFile;
 module.exports.SqliteConnection = SqliteConnection;
+module.exports.ValidationResult = ValidationResult;
diff --git a/packages/native/package.json b/packages/native/package.json
index 43692d819d..aaa2f8ce37 100644
--- a/packages/native/package.json
+++ b/packages/native/package.json
@@ -11,6 +11,9 @@
         "aarch64-unknown-linux-gnu",
         "aarch64-pc-windows-msvc"
       ]
+    },
+    "ts": {
+      "constEnum": false
     }
   },
   "license": "MPL-2.0",
@@ -29,8 +32,8 @@
   },
   "scripts": {
     "artifacts": "napi artifacts",
-    "build": "napi build --platform --release",
-    "build:debug": "napi build --platform",
+    "build": "napi build --platform --release --no-const-enum",
+    "build:debug": "napi build --platform --no-const-enum",
     "universal": "napi universal",
     "test": "cross-env TS_NODE_TRANSPILE_ONLY=1 TS_NODE_PROJECT=./tsconfig.json node --test --loader ts-node/esm --experimental-specifier-resolution=node ./__tests__/**/*.mts",
     "version": "napi version"
diff --git a/packages/native/src/sqlite/mod.rs b/packages/native/src/sqlite/mod.rs
index 066114ea3f..d82243d01d 100644
--- a/packages/native/src/sqlite/mod.rs
+++ b/packages/native/src/sqlite/mod.rs
@@ -1,5 +1,5 @@
 use chrono::NaiveDateTime;
-use napi::bindgen_prelude::{Buffer, Uint8Array};
+use napi::bindgen_prelude::{Buffer, FromNapiValue, ToNapiValue, Uint8Array};
 use napi_derive::napi;
 use sqlx::{
   migrate::MigrateDatabase,
@@ -34,6 +34,14 @@ pub struct SqliteConnection {
   path: String,
 }
 
+#[napi]
+pub enum ValidationResult {
+  MissingTables,
+  MissingDocIdColumn,
+  GeneralError,
+  Valid,
+}
+
 #[napi]
 impl SqliteConnection {
   #[napi(constructor)]
@@ -231,14 +239,14 @@ impl SqliteConnection {
   }
 
   #[napi]
-  pub async fn validate(path: String) -> bool {
+  pub async fn validate(path: String) -> ValidationResult {
     let pool = match SqlitePoolOptions::new()
       .max_connections(1)
       .connect(&path)
       .await
     {
       Ok(pool) => pool,
-      Err(_) => return false,
+      Err(_) => return ValidationResult::GeneralError,
     };
 
     let tables_res = sqlx::query("SELECT name FROM sqlite_master WHERE type='table'")
@@ -250,26 +258,32 @@ impl SqliteConnection {
         let names: Vec<String> = res.iter().map(|row| row.get(0)).collect();
         names.contains(&"updates".to_string()) && names.contains(&"blobs".to_string())
       }
-      Err(_) => return false,
+      Err(_) => return ValidationResult::GeneralError,
     };
 
     let columns_res = sqlx::query("PRAGMA table_info(updates)")
       .fetch_all(&pool)
       .await;
 
-    let columns_exist = match columns_res {
+    let doc_id_exist = match columns_res {
       Ok(res) => {
         let names: Vec<String> = res.iter().map(|row| row.get(1)).collect();
-        names.contains(&"data".to_string()) && names.contains(&"doc_id".to_string())
+        names.contains(&"doc_id".to_string())
       }
-      Err(_) => return false,
+      Err(_) => return ValidationResult::GeneralError,
     };
 
-    tables_exist && columns_exist
+    if !tables_exist {
+      ValidationResult::MissingTables
+    } else if !doc_id_exist {
+      ValidationResult::MissingDocIdColumn
+    } else {
+      ValidationResult::Valid
+    }
   }
 
-  // todo: have a better way to handle migration
-  async fn migrate_add_doc_id(&self) -> Result<(), anyhow::Error> {
+  #[napi]
+  pub async fn migrate_add_doc_id(&self) -> napi::Result<()> {
     // ignore errors
     match sqlx::query("ALTER TABLE updates ADD COLUMN doc_id TEXT")
       .execute(&self.pool)
@@ -280,7 +294,7 @@ impl SqliteConnection {
         if err.to_string().contains("duplicate column name") {
           Ok(()) // Ignore error if it's due to duplicate column
         } else {
-          Err(anyhow::Error::from(err)) // Propagate other errors
+          Err(anyhow::Error::from(err).into()) // Propagate other errors
         }
       }
     }
diff --git a/vitest.config.ts b/vitest.config.ts
index 5993101e59..c6b955a0b2 100644
--- a/vitest.config.ts
+++ b/vitest.config.ts
@@ -1,4 +1,4 @@
-import { resolve } from 'node:path';
+import path, { resolve } from 'node:path';
 import { fileURLToPath } from 'node:url';
 
 import { vanillaExtractPlugin } from '@vanilla-extract/vite-plugin';
@@ -15,6 +15,8 @@ export default defineConfig({
     alias: {
       'next/router': 'next-router-mock',
       'next/config': resolve(rootDir, './scripts/vitest/next-config-mock.ts'),
+      // prevent tests using two different sources of yjs
+      yjs: path.resolve(__dirname, 'node_modules/yjs'),
     },
   },
   define: {
diff --git a/yarn.lock b/yarn.lock
index 11320faada..708a60e230 100644
--- a/yarn.lock
+++ b/yarn.lock
@@ -211,6 +211,7 @@ __metadata:
   resolution: "@affine/electron@workspace:apps/electron"
   dependencies:
     "@affine-test/kit": "workspace:*"
+    "@affine/env": "workspace:*"
     "@affine/native": "workspace:*"
     "@blocksuite/blocks": 0.0.0-20230705162600-2cb608e4-nightly
     "@blocksuite/editor": 0.0.0-20230705162600-2cb608e4-nightly