diff --git a/.changeset/three-baboons-hunt.md b/.changeset/three-baboons-hunt.md
new file mode 100644
index 0000000000..1909b6f51b
--- /dev/null
+++ b/.changeset/three-baboons-hunt.md
@@ -0,0 +1,23 @@
+---
+"@lynx-js/rspeedy": patch
+---
+
+Enable native Rsdoctor plugin by default.
+
+Set `tools.rsdoctor.experiments.enableNativePlugin` to `false` to use the old JS plugin.
+
+```js
+import { defineConfig } from '@lynx-js/rspeedy';
+
+export default defineConfig({
+  tools: {
+    rsdoctor: {
+      experiments: {
+        enableNativePlugin: false,
+      },
+    },
+  },
+});
+```
+
+See [Rsdoctor - 1.0](https://rsdoctor.dev/blog/release/release-note-1_0#-faster-analysis) for more details.
diff --git a/packages/rspeedy/core/src/config/defaults.ts b/packages/rspeedy/core/src/config/defaults.ts
index b717d8baf5..e387826ea1 100644
--- a/packages/rspeedy/core/src/config/defaults.ts
+++ b/packages/rspeedy/core/src/config/defaults.ts
@@ -8,14 +8,22 @@ import type { Filename } from './output/filename.js'
 import type { Config } from './index.js'
 
 export function applyDefaultRspeedyConfig(config: Config): Config {
-  const ret = mergeRsbuildConfig(config, {
+  const ret = mergeRsbuildConfig({
     output: {
       // We are applying the default filename to the config
       // since some plugin(e.g.: `@lynx-js/qrcode-rsbuild-plugin`) will read
       // from the `output.filename.bundle` field.
       filename: getFilename(config.output?.filename),
     },
-  })
+
+    tools: {
+      rsdoctor: {
+        experiments: {
+          enableNativePlugin: true,
+        },
+      },
+    },
+  }, config)
 
   return ret
 }
diff --git a/packages/rspeedy/core/test/config/tools/tools.test-d.ts b/packages/rspeedy/core/test/config/tools/tools.test-d.ts
index 3f94af0835..36d61d7472 100644
--- a/packages/rspeedy/core/test/config/tools/tools.test-d.ts
+++ b/packages/rspeedy/core/test/config/tools/tools.test-d.ts
@@ -160,6 +160,28 @@ describe('Config - Tools', () => {
     })
   })
 
+  test('tools.rsdoctor', () => {
+    assertType<Tools>({
+      rsdoctor: {},
+    })
+
+    assertType<Tools>({
+      rsdoctor: {
+        experiments: {
+          enableNativePlugin: true,
+        },
+      },
+    })
+
+    assertType<Tools>({
+      rsdoctor: {
+        experiments: {
+          enableNativePlugin: false,
+        },
+      },
+    })
+  })
+
   test('tools.rspack', () => {
     // Object
     assertType<Tools>({
diff --git a/packages/rspeedy/core/test/plugins/output.plugin.test.ts b/packages/rspeedy/core/test/plugins/output.plugin.test.ts
index 39ca93dfb7..b654932295 100644
--- a/packages/rspeedy/core/test/plugins/output.plugin.test.ts
+++ b/packages/rspeedy/core/test/plugins/output.plugin.test.ts
@@ -698,12 +698,7 @@ describe('Plugins - Output', () => {
       await rsbuild.unwrapConfig()
 
       expect(rsbuild.getRspeedyConfig().output?.filename).toMatchInlineSnapshot(
-        `
-        {
-          "bundle": "static/bundle/[name].bundle",
-          "template": "static/bundle/[name].bundle",
-        }
-      `,
+        `"static/bundle/[name].bundle"`,
       )
     })
 
@@ -758,7 +753,7 @@ describe('Plugins - Output', () => {
         .toMatchInlineSnapshot(`
           {
             "bundle": "[name].bundle",
-            "template": "[name].bundle",
+            "template": "[name].template",
           }
         `)
     })
diff --git a/packages/rspeedy/core/test/plugins/rsdoctor.plugin.test.ts b/packages/rspeedy/core/test/plugins/rsdoctor.plugin.test.ts
index 5a22a49d51..b84a8fb71c 100644
--- a/packages/rspeedy/core/test/plugins/rsdoctor.plugin.test.ts
+++ b/packages/rspeedy/core/test/plugins/rsdoctor.plugin.test.ts
@@ -29,6 +29,33 @@ describe('Plugins - Rsdoctor', () => {
     })
 
     expect(options.supports.banner).toBe(true)
+
+    expect(options.experiments?.enableNativePlugin).toBe(true)
+  })
+
+  test('experiments.enableNativePlugin: false', async () => {
+    vi.stubEnv('RSDOCTOR', 'true')
+
+    const { createStubRspeedy } = await import('../createStubRspeedy.js')
+
+    const rsbuild = await createStubRspeedy({
+      tools: {
+        rsdoctor: {
+          experiments: {
+            enableNativePlugin: false,
+          },
+        },
+      },
+    })
+
+    const compiler = await rsbuild.createCompiler<Rspack.Compiler>()
+
+    const { options } = compiler.options.plugins.find(
+      (plugin) => (typeof plugin === 'object'
+        && plugin?.['isRsdoctorPlugin'] === true),
+    ) as RsdoctorRspackPlugin<[]>
+
+    expect(options.experiments?.enableNativePlugin).toBe(false)
   })
 
   test('linter.rules.ecma-version-check', async () => {