diff --git a/packages/backend/server/migrations/20250509070728_add_workspace_sid_and_indexed/migration.sql b/packages/backend/server/migrations/20250509070728_add_workspace_sid_and_indexed/migration.sql
new file mode 100644
index 0000000000..43d84e34b6
--- /dev/null
+++ b/packages/backend/server/migrations/20250509070728_add_workspace_sid_and_indexed/migration.sql
@@ -0,0 +1,14 @@
+/*
+  Warnings:
+
+  - A unique constraint covering the columns `[sid]` on the table `workspaces` will be added. If there are existing duplicate values, this will fail.
+
+*/
+-- AlterTable
+ALTER TABLE "workspaces" ADD COLUMN "sid" INT GENERATED BY DEFAULT AS IDENTITY;
+
+-- CreateIndex
+CREATE UNIQUE INDEX "workspaces_sid_key" ON "workspaces"("sid");
+
+-- AlterTable
+ALTER TABLE "workspaces" ADD COLUMN     "indexed" BOOLEAN NOT NULL DEFAULT false;
diff --git a/packages/backend/server/schema.prisma b/packages/backend/server/schema.prisma
index 166f28941d..ad4da0ad53 100644
--- a/packages/backend/server/schema.prisma
+++ b/packages/backend/server/schema.prisma
@@ -106,6 +106,8 @@ model VerificationToken {
 }
 
 model Workspace {
+  // NOTE: manually set this column type to identity in migration file
+  sid                Int      @unique @default(autoincrement())
   id                 String   @id @default(uuid()) @db.VarChar
   public             Boolean
   createdAt          DateTime @default(now()) @map("created_at") @db.Timestamptz(3)
@@ -115,6 +117,7 @@ model Workspace {
   enableDocEmbedding Boolean  @default(true) @map("enable_doc_embedding")
   name               String?  @db.VarChar
   avatarKey          String?  @map("avatar_key") @db.VarChar
+  indexed            Boolean  @default(false)
 
   features       WorkspaceFeature[]
   docs           WorkspaceDoc[]
diff --git a/packages/backend/server/src/__tests__/mocks/doc-snapshot.mock.ts b/packages/backend/server/src/__tests__/mocks/doc-snapshot.mock.ts
index 16a1bbb1ad..ac8ae5295e 100644
--- a/packages/backend/server/src/__tests__/mocks/doc-snapshot.mock.ts
+++ b/packages/backend/server/src/__tests__/mocks/doc-snapshot.mock.ts
@@ -11,6 +11,7 @@ export type MockDocSnapshotInput = {
   workspaceId: string;
   docId?: string;
   blob?: Uint8Array;
+  updatedAt?: Date;
 };
 
 export type MockedDocSnapshot = Snapshot;
@@ -32,7 +33,7 @@ export class MockDocSnapshot extends Mocker<
         workspaceId: input.workspaceId,
         blob: input.blob,
         createdAt: new Date(),
-        updatedAt: new Date(),
+        updatedAt: input.updatedAt ?? new Date(),
         createdBy: input.user.id,
         updatedBy: input.user.id,
       },
diff --git a/packages/backend/server/src/base/job/queue/executor.ts b/packages/backend/server/src/base/job/queue/executor.ts
index 71e8e2e69a..183c7fe2dd 100644
--- a/packages/backend/server/src/base/job/queue/executor.ts
+++ b/packages/backend/server/src/base/job/queue/executor.ts
@@ -161,7 +161,12 @@ export class JobExecutor implements OnModuleDestroy {
   async handleJobReturn(job: Job, result: JOB_SIGNAL) {
     if (result === JOB_SIGNAL.Repeat || result === JOB_SIGNAL.Retry) {
       try {
-        await this.getQueue(job.name).add(job.name, job.data, job.opts);
+        await this.getQueue(namespace(job.name as JobName)).add(
+          job.name,
+          job.data,
+          job.opts
+        );
+        this.logger.debug(`Added job [${job.name}] to queue, signal=${result}`);
       } catch (e) {
         this.logger.error(`Failed to add job [${job.name}]`, e);
       }
diff --git a/packages/backend/server/src/models/doc.ts b/packages/backend/server/src/models/doc.ts
index 148a9e0d82..8edc302497 100644
--- a/packages/backend/server/src/models/doc.ts
+++ b/packages/backend/server/src/models/doc.ts
@@ -171,15 +171,20 @@ export class DocModel extends BaseModel {
     };
   }
 
-  async getSnapshot(workspaceId: string, docId: string) {
-    return await this.db.snapshot.findUnique({
+  async getSnapshot<Select extends Prisma.SnapshotSelect>(
+    workspaceId: string,
+    docId: string,
+    options?: { select?: Select }
+  ) {
+    return (await this.db.snapshot.findUnique({
       where: {
         workspaceId_id: {
           workspaceId,
           id: docId,
         },
       },
-    });
+      select: options?.select,
+    })) as Prisma.SnapshotGetPayload<{ select: Select }> | null;
   }
 
   async getAuthors(workspaceId: string, docId: string) {
diff --git a/packages/backend/server/src/models/workspace.ts b/packages/backend/server/src/models/workspace.ts
index 062ab07c61..5952da16b5 100644
--- a/packages/backend/server/src/models/workspace.ts
+++ b/packages/backend/server/src/models/workspace.ts
@@ -22,6 +22,7 @@ export type UpdateWorkspaceInput = Pick<
   | 'enableDocEmbedding'
   | 'name'
   | 'avatarKey'
+  | 'indexed'
 >;
 
 @Injectable()
@@ -54,7 +55,7 @@ export class WorkspaceModel extends BaseModel {
       },
       data,
     });
-    this.logger.log(
+    this.logger.debug(
       `Updated workspace ${workspaceId} with data ${JSON.stringify(data)}`
     );
     return workspace;
@@ -76,6 +77,18 @@ export class WorkspaceModel extends BaseModel {
     });
   }
 
+  async listAfterSid(sid: number, limit: number) {
+    return await this.db.workspace.findMany({
+      where: {
+        sid: { gt: sid },
+      },
+      take: limit,
+      orderBy: {
+        sid: 'asc',
+      },
+    });
+  }
+
   async delete(workspaceId: string) {
     const rawResult = await this.db.workspace.deleteMany({
       where: {
diff --git a/packages/backend/server/src/plugins/indexer/__tests__/job.spec.ts b/packages/backend/server/src/plugins/indexer/__tests__/job.spec.ts
index ab338a3ccb..e2d9eb0641 100644
--- a/packages/backend/server/src/plugins/indexer/__tests__/job.spec.ts
+++ b/packages/backend/server/src/plugins/indexer/__tests__/job.spec.ts
@@ -6,7 +6,9 @@ import Sinon from 'sinon';
 
 import { createModule } from '../../../__tests__/create-module';
 import { Mockers } from '../../../__tests__/mocks';
+import { JOB_SIGNAL } from '../../../base';
 import { ServerConfigModule } from '../../../core/config';
+import { Models } from '../../../models';
 import { IndexerModule, IndexerService } from '..';
 import { SearchProviderFactory } from '../factory';
 import { IndexerJob } from '../job';
@@ -20,6 +22,7 @@ const indexerService = module.get(IndexerService);
 const indexerJob = module.get(IndexerJob);
 const searchProviderFactory = module.get(SearchProviderFactory);
 const manticoresearch = module.get(ManticoresearchProvider);
+const models = module.get(Models);
 
 const user = await module.create(Mockers.User);
 const workspace = await module.create(Mockers.Workspace, {
@@ -63,15 +66,21 @@ test('should handle indexer.deleteDoc job', async t => {
 test('should handle indexer.indexWorkspace job', async t => {
   const count = module.queue.count('indexer.deleteDoc');
   const spy = Sinon.spy(indexerService, 'listDocIds');
+
   await indexerJob.indexWorkspace({
     workspaceId: workspace.id,
   });
+
   t.is(spy.callCount, 1);
   const { payload } = await module.queue.waitFor('indexer.indexDoc');
   t.is(payload.workspaceId, workspace.id);
   t.is(payload.docId, '5nS9BSp3Px');
   // no delete job
   t.is(module.queue.count('indexer.deleteDoc'), count);
+
+  // workspace should be indexed
+  const ws = await models.workspace.get(workspace.id);
+  t.is(ws!.indexed, true);
 });
 
 test('should not sync existing doc', async t => {
@@ -79,9 +88,11 @@ test('should not sync existing doc', async t => {
   mock.method(indexerService, 'listDocIds', async () => {
     return ['5nS9BSp3Px'];
   });
+
   await indexerJob.indexWorkspace({
     workspaceId: workspace.id,
   });
+
   t.is(module.queue.count('indexer.indexDoc'), count);
 });
 
@@ -90,9 +101,11 @@ test('should delete doc from indexer when docId is not in workspace', async t =>
   mock.method(indexerService, 'listDocIds', async () => {
     return ['mock-doc-id1', 'mock-doc-id2'];
   });
+
   await indexerJob.indexWorkspace({
     workspaceId: workspace.id,
   });
+
   const { payload } = await module.queue.waitFor('indexer.indexDoc');
   t.is(payload.workspaceId, workspace.id);
   t.is(payload.docId, '5nS9BSp3Px');
@@ -101,8 +114,71 @@ test('should delete doc from indexer when docId is not in workspace', async t =>
 
 test('should handle indexer.deleteWorkspace job', async t => {
   const spy = Sinon.spy(indexerService, 'deleteWorkspace');
+
   await indexerJob.deleteWorkspace({
     workspaceId: workspace.id,
   });
+
   t.is(spy.callCount, 1);
 });
+
+test('should handle indexer.autoIndexWorkspaces job', async t => {
+  const workspace = await module.create(Mockers.Workspace, {
+    snapshot: true,
+  });
+
+  const result = await indexerJob.autoIndexWorkspaces({
+    lastIndexedWorkspaceSid: workspace.sid - 1,
+  });
+  t.is(result, JOB_SIGNAL.Repeat);
+
+  const { payload } = await module.queue.waitFor('indexer.indexWorkspace');
+  t.is(payload.workspaceId, workspace.id);
+
+  // no new auto index job
+  const count = module.queue.count('indexer.autoIndexWorkspaces');
+
+  await indexerJob.autoIndexWorkspaces({
+    lastIndexedWorkspaceSid: workspace.sid,
+  });
+
+  t.is(module.queue.count('indexer.autoIndexWorkspaces'), count);
+});
+
+test('should not index workspace if it is not updated in 180 days', async t => {
+  const workspace = await module.create(Mockers.Workspace);
+  await module.create(Mockers.DocSnapshot, {
+    user,
+    workspaceId: workspace.id,
+    docId: workspace.id,
+    updatedAt: new Date(Date.now() - 180 * 24 * 60 * 60 * 1000 - 1),
+  });
+
+  const count = module.queue.count('indexer.indexWorkspace');
+
+  await indexerJob.autoIndexWorkspaces({
+    lastIndexedWorkspaceSid: workspace.sid - 1,
+  });
+
+  t.is(module.queue.count('indexer.indexWorkspace'), count);
+});
+
+test('should not index workspace if snapshot not exists', async t => {
+  // not create snapshot
+  const workspace = await module.create(Mockers.Workspace);
+
+  const count = module.queue.count('indexer.indexWorkspace');
+
+  await indexerJob.autoIndexWorkspaces({
+    lastIndexedWorkspaceSid: workspace.sid - 1,
+  });
+
+  t.is(module.queue.count('indexer.indexWorkspace'), count);
+});
+
+test('should schedule auto index workspaces', async t => {
+  await indexerJob.scheduleAutoIndexWorkspaces();
+
+  const { payload } = await module.queue.waitFor('indexer.autoIndexWorkspaces');
+  t.is(payload.lastIndexedWorkspaceSid, undefined);
+});
diff --git a/packages/backend/server/src/plugins/indexer/job.ts b/packages/backend/server/src/plugins/indexer/job.ts
index d94fc9e5a5..ed8ad18531 100644
--- a/packages/backend/server/src/plugins/indexer/job.ts
+++ b/packages/backend/server/src/plugins/indexer/job.ts
@@ -1,6 +1,7 @@
 import { Injectable, Logger } from '@nestjs/common';
+import { Cron, CronExpression } from '@nestjs/schedule';
 
-import { JobQueue, OnJob } from '../../base';
+import { Config, JOB_SIGNAL, JobQueue, OnJob } from '../../base';
 import { readAllDocIdsFromWorkspaceSnapshot } from '../../core/utils/blocksuite';
 import { Models } from '../../models';
 import { IndexerService } from './service';
@@ -21,6 +22,9 @@ declare global {
     'indexer.deleteWorkspace': {
       workspaceId: string;
     };
+    'indexer.autoIndexWorkspaces': {
+      lastIndexedWorkspaceSid?: number;
+    };
   }
 }
 
@@ -31,7 +35,8 @@ export class IndexerJob {
   constructor(
     private readonly models: Models,
     private readonly service: IndexerService,
-    private readonly queue: JobQueue
+    private readonly queue: JobQueue,
+    private readonly config: Config
   ) {}
 
   @OnJob('indexer.indexDoc')
@@ -51,22 +56,30 @@ export class IndexerJob {
   @OnJob('indexer.indexWorkspace')
   async indexWorkspace({ workspaceId }: Jobs['indexer.indexWorkspace']) {
     await this.queue.remove(workspaceId, 'indexer.deleteWorkspace');
+    const workspace = await this.models.workspace.get(workspaceId);
+    if (!workspace) {
+      this.logger.warn(`workspace ${workspaceId} not found`);
+      return;
+    }
+
     const snapshot = await this.models.doc.getSnapshot(
       workspaceId,
       workspaceId
     );
     if (!snapshot) {
-      this.logger.warn(`workspace ${workspaceId} not found`);
+      this.logger.warn(`workspace snapshot ${workspaceId} not found`);
       return;
     }
+
     const docIdsInWorkspace = readAllDocIdsFromWorkspaceSnapshot(snapshot.blob);
     const docIdsInIndexer = await this.service.listDocIds(workspaceId);
+
     const docIdsInWorkspaceSet = new Set(docIdsInWorkspace);
     const docIdsInIndexerSet = new Set(docIdsInIndexer);
-    // diff the docIdsInWorkspace and docIdsInIndexer
-    const missingDocIds = docIdsInWorkspace.filter(
-      docId => !docIdsInIndexerSet.has(docId)
-    );
+    // diff the docIdsInWorkspace and docIdsInIndexer, if the workspace is not indexed, all the docIdsInWorkspace should be indexed
+    const missingDocIds = workspace.indexed
+      ? docIdsInWorkspace.filter(docId => !docIdsInIndexerSet.has(docId))
+      : docIdsInWorkspace;
     const deletedDocIds = docIdsInIndexer.filter(
       docId => !docIdsInWorkspaceSet.has(docId)
     );
@@ -97,6 +110,11 @@ export class IndexerJob {
         }
       );
     }
+    if (!workspace.indexed) {
+      await this.models.workspace.update(workspaceId, {
+        indexed: true,
+      });
+    }
     this.logger.debug(
       `indexed workspace ${workspaceId} with ${missingDocIds.length} missing docs and ${deletedDocIds.length} deleted docs`
     );
@@ -107,4 +125,67 @@ export class IndexerJob {
     await this.queue.remove(workspaceId, 'indexer.indexWorkspace');
     await this.service.deleteWorkspace(workspaceId);
   }
+
+  @OnJob('indexer.autoIndexWorkspaces')
+  async autoIndexWorkspaces(payload: Jobs['indexer.autoIndexWorkspaces']) {
+    const startSid = payload.lastIndexedWorkspaceSid ?? 0;
+    const workspaces = await this.models.workspace.listAfterSid(startSid, 100);
+    if (workspaces.length === 0) {
+      // Keep the current sid value when repeating
+      return JOB_SIGNAL.Repeat;
+    }
+    let addedCount = 0;
+    for (const workspace of workspaces) {
+      if (workspace.indexed) {
+        continue;
+      }
+      const snapshotMeta = await this.models.doc.getSnapshot(
+        workspace.id,
+        workspace.id,
+        {
+          select: {
+            updatedAt: true,
+          },
+        }
+      );
+      // ignore 180 days not updated workspaces
+      if (
+        !snapshotMeta?.updatedAt ||
+        Date.now() - snapshotMeta.updatedAt.getTime() >
+          180 * 24 * 60 * 60 * 1000
+      ) {
+        continue;
+      }
+      await this.queue.add(
+        'indexer.indexWorkspace',
+        { workspaceId: workspace.id },
+        { jobId: workspace.id }
+      );
+      addedCount++;
+    }
+    const nextSid = workspaces[workspaces.length - 1].sid;
+    this.logger.log(
+      `Auto added ${addedCount} workspaces to queue, lastIndexedWorkspaceSid: ${startSid} -> ${nextSid}`
+    );
+
+    // update the lastIndexedWorkspaceSid in the payload and repeat the job after 30 seconds
+    payload.lastIndexedWorkspaceSid = nextSid;
+    return JOB_SIGNAL.Repeat;
+  }
+
+  @Cron(CronExpression.EVERY_30_SECONDS)
+  async scheduleAutoIndexWorkspaces() {
+    if (!this.config.indexer.enabled) {
+      return;
+    }
+    await this.queue.add(
+      'indexer.autoIndexWorkspaces',
+      {},
+      {
+        // make sure only one job is running at a time
+        delay: 30 * 1000,
+        jobId: 'indexer:auto-index-workspaces',
+      }
+    );
+  }
 }