diff --git a/blocksuite/affine/all/src/__tests__/adapters/markdown.unit.spec.ts b/blocksuite/affine/all/src/__tests__/adapters/markdown.unit.spec.ts
index 26df93f952..b5531145eb 100644
--- a/blocksuite/affine/all/src/__tests__/adapters/markdown.unit.spec.ts
+++ b/blocksuite/affine/all/src/__tests__/adapters/markdown.unit.spec.ts
@@ -4417,6 +4417,69 @@ hhh
       });
       expect(nanoidReplacement(rawBlockSnapshot)).toEqual(blockSnapshot);
     });
+
+    test('should handle footnote reference with url prefix', async () => {
+      const blockSnapshot = {
+        type: 'block',
+        id: 'matchesReplaceMap[0]',
+        flavour: 'affine:note',
+        props: {
+          xywh: '[0,0,800,95]',
+          background: DefaultTheme.noteBackgrounColor,
+          index: 'a0',
+          hidden: false,
+          displayMode: NoteDisplayMode.DocAndEdgeless,
+        },
+        children: [
+          {
+            type: 'block',
+            id: 'matchesReplaceMap[1]',
+            flavour: 'affine:paragraph',
+            props: {
+              type: 'text',
+              text: {
+                '$blocksuite:internal:text$': true,
+                delta: [
+                  {
+                    insert: 'https://example.com',
+                    attributes: {
+                      link: 'https://example.com',
+                    },
+                  },
+                  {
+                    insert: ' ',
+                  },
+                  {
+                    insert: ' ',
+                    attributes: {
+                      footnote: {
+                        label: '1',
+                        reference: {
+                          type: 'url',
+                          url,
+                          favicon,
+                          title,
+                          description,
+                        },
+                      },
+                    },
+                  },
+                ],
+              },
+            },
+            children: [],
+          },
+        ],
+      };
+
+      const markdown = `https://example.com[^1]\n\n[^1]: {"type":"url","url":"${url}","favicon":"${favicon}","title":"${title}","description":"${description}"}\n`;
+
+      const mdAdapter = new MarkdownAdapter(createJob(), provider);
+      const rawBlockSnapshot = await mdAdapter.toBlockSnapshot({
+        file: markdown,
+      });
+      expect(nanoidReplacement(rawBlockSnapshot)).toEqual(blockSnapshot);
+    });
   });
 
   test('should not wrap url with angle brackets if it is not a url', async () => {
diff --git a/blocksuite/affine/inlines/footnote/package.json b/blocksuite/affine/inlines/footnote/package.json
index 51e7cfb073..5a44a046cb 100644
--- a/blocksuite/affine/inlines/footnote/package.json
+++ b/blocksuite/affine/inlines/footnote/package.json
@@ -33,6 +33,9 @@
     "yjs": "^13.6.21",
     "zod": "^3.23.8"
   },
+  "devDependencies": {
+    "vitest": "3.1.3"
+  },
   "exports": {
     ".": "./src/index.ts",
     "./view": "./src/view.ts",
diff --git a/blocksuite/affine/inlines/footnote/src/__tests__/adapters/preprocessor.unit.spec.ts b/blocksuite/affine/inlines/footnote/src/__tests__/adapters/preprocessor.unit.spec.ts
new file mode 100644
index 0000000000..5ef0f62cea
--- /dev/null
+++ b/blocksuite/affine/inlines/footnote/src/__tests__/adapters/preprocessor.unit.spec.ts
@@ -0,0 +1,66 @@
+import { describe, expect, it } from 'vitest';
+
+import { preprocessFootnoteReference } from '../../adapters/markdown/preprocessor';
+
+describe('FootnoteReferenceMarkdownPreprocessorExtension', () => {
+  it('should add space before footnote reference when it follows a URL', () => {
+    const content = 'https://example.com[^label]';
+    const expected = 'https://example.com [^label]';
+    expect(preprocessFootnoteReference(content)).toBe(expected);
+  });
+
+  it('should add space before footnote reference when URL has text prefix with space', () => {
+    const content = 'hello world https://example.com[^label]';
+    const expected = 'hello world https://example.com [^label]';
+    expect(preprocessFootnoteReference(content)).toBe(expected);
+  });
+
+  it('should add space before footnote reference when URL has text prefix with dash', () => {
+    const content = 'text-https://example.com[^label]';
+    const expected = 'text-https://example.com [^label]';
+    expect(preprocessFootnoteReference(content)).toBe(expected);
+  });
+
+  it('should not add space when footnote reference follows non-URL text', () => {
+    const content = 'normal text[^label]';
+    const expected = 'normal text[^label]';
+    expect(preprocessFootnoteReference(content)).toBe(expected);
+  });
+
+  it('should not add space when there is already a space before footnote reference', () => {
+    const content = 'https://example.com [^label]';
+    const expected = 'https://example.com [^label]';
+    expect(preprocessFootnoteReference(content)).toBe(expected);
+  });
+
+  it('should handle multiple footnote references with mixed URL and non-URL text', () => {
+    const content = 'https://example.com[^1]normal text[^2]http://test.com[^3]';
+    const expected =
+      'https://example.com [^1]normal text[^2]http://test.com [^3]';
+    expect(preprocessFootnoteReference(content)).toBe(expected);
+  });
+
+  it('should not modify footnote definitions', () => {
+    const content = '[^label]: This is a footnote definition';
+    const expected = '[^label]: This is a footnote definition';
+    expect(preprocessFootnoteReference(content)).toBe(expected);
+  });
+
+  it('should handle content without footnote references', () => {
+    const content = 'This is a normal text without any footnotes';
+    const expected = 'This is a normal text without any footnotes';
+    expect(preprocessFootnoteReference(content)).toBe(expected);
+  });
+
+  it('should handle complex URLs with paths and parameters', () => {
+    const content = 'https://example.com/path?param=value[^label]';
+    const expected = 'https://example.com/path?param=value [^label]';
+    expect(preprocessFootnoteReference(content)).toBe(expected);
+  });
+
+  it('should handle invalid URLs', () => {
+    const content = 'not-a-url[^label]';
+    const expected = 'not-a-url[^label]';
+    expect(preprocessFootnoteReference(content)).toBe(expected);
+  });
+});
diff --git a/blocksuite/affine/inlines/footnote/src/adapters/index.ts b/blocksuite/affine/inlines/footnote/src/adapters/index.ts
index 7264039840..ffa82fff1a 100644
--- a/blocksuite/affine/inlines/footnote/src/adapters/index.ts
+++ b/blocksuite/affine/inlines/footnote/src/adapters/index.ts
@@ -1,2 +1,3 @@
 export * from './markdown/inline-delta';
 export * from './markdown/markdown-inline';
+export * from './markdown/preprocessor';
diff --git a/blocksuite/affine/inlines/footnote/src/adapters/markdown/preprocessor.ts b/blocksuite/affine/inlines/footnote/src/adapters/markdown/preprocessor.ts
new file mode 100644
index 0000000000..4db7e06a35
--- /dev/null
+++ b/blocksuite/affine/inlines/footnote/src/adapters/markdown/preprocessor.ts
@@ -0,0 +1,54 @@
+import {
+  type MarkdownAdapterPreprocessor,
+  MarkdownPreprocessorExtension,
+} from '@blocksuite/affine-shared/adapters';
+
+/**
+ * Check if a string is a URL
+ * @param str
+ * @returns
+ */
+function isUrl(str: string): boolean {
+  try {
+    new URL(str);
+    return true;
+  } catch {
+    return false;
+  }
+}
+
+/**
+ * Preprocess footnote references to avoid markdown link parsing
+ * Only add space when footnote reference follows a URL
+ * @param content
+ * @returns
+ * @example
+ * ```md
+ * https://example.com[^label] -> https://example.com [^label]
+ * normal text[^label] -> normal text[^label]
+ * ```
+ */
+export function preprocessFootnoteReference(content: string) {
+  return content.replace(
+    /([^\s]+?)(\[\^[^\]]+\])(?!:)/g,
+    (match, prevText, footnoteRef) => {
+      // Only add space if the previous text is a URL
+      if (isUrl(prevText)) {
+        return prevText + ' ' + footnoteRef;
+      }
+      // Otherwise return the original match
+      return match;
+    }
+  );
+}
+
+const footnoteReferencePreprocessor: MarkdownAdapterPreprocessor = {
+  name: 'footnote-reference',
+  levels: ['block', 'slice', 'doc'],
+  preprocess: content => {
+    return preprocessFootnoteReference(content);
+  },
+};
+
+export const FootnoteReferenceMarkdownPreprocessorExtension =
+  MarkdownPreprocessorExtension(footnoteReferencePreprocessor);
diff --git a/blocksuite/affine/inlines/footnote/src/store.ts b/blocksuite/affine/inlines/footnote/src/store.ts
index 2826f2f7be..85a7bf0d4f 100644
--- a/blocksuite/affine/inlines/footnote/src/store.ts
+++ b/blocksuite/affine/inlines/footnote/src/store.ts
@@ -5,6 +5,7 @@ import {
 
 import {
   footnoteReferenceDeltaToMarkdownAdapterMatcher,
+  FootnoteReferenceMarkdownPreprocessorExtension,
   markdownFootnoteReferenceToDeltaMatcher,
 } from './adapters';
 
@@ -15,5 +16,6 @@ export class FootnoteStoreExtension extends StoreExtensionProvider {
     super.setup(context);
     context.register(markdownFootnoteReferenceToDeltaMatcher);
     context.register(footnoteReferenceDeltaToMarkdownAdapterMatcher);
+    context.register(FootnoteReferenceMarkdownPreprocessorExtension);
   }
 }
diff --git a/blocksuite/affine/inlines/footnote/vitest.config.ts b/blocksuite/affine/inlines/footnote/vitest.config.ts
new file mode 100644
index 0000000000..05591362f9
--- /dev/null
+++ b/blocksuite/affine/inlines/footnote/vitest.config.ts
@@ -0,0 +1,25 @@
+import { defineConfig } from 'vitest/config';
+
+export default defineConfig({
+  esbuild: {
+    target: 'es2018',
+  },
+  test: {
+    browser: {
+      enabled: true,
+      headless: true,
+      name: 'chromium',
+      provider: 'playwright',
+      isolate: false,
+      providerOptions: {},
+    },
+    include: ['src/__tests__/**/*.unit.spec.ts'],
+    testTimeout: 500,
+    coverage: {
+      provider: 'istanbul',
+      reporter: ['lcov'],
+      reportsDirectory: '../../../.coverage/footnote',
+    },
+    restoreMocks: true,
+  },
+});
diff --git a/yarn.lock b/yarn.lock
index dfa162efff..e9880e395a 100644
--- a/yarn.lock
+++ b/yarn.lock
@@ -3480,6 +3480,7 @@ __metadata:
     lit-html: "npm:^3.2.1"
     lodash-es: "npm:^4.17.21"
     rxjs: "npm:^7.8.1"
+    vitest: "npm:3.1.3"
     yjs: "npm:^13.6.21"
     zod: "npm:^3.23.8"
   languageName: unknown