diff --git a/packages/core/src/config.ts b/packages/core/src/config.ts
index d194a64d5..2d63d53f3 100644
--- a/packages/core/src/config.ts
+++ b/packages/core/src/config.ts
@@ -730,16 +730,24 @@ const composeAutoExtensionConfig = (
     autoExtension,
   });
 
-  return {
-    config: {
-      output: {
-        filename: {
-          js: `[name]${jsExtension}`,
-          ...config.output?.filename,
-        },
+  const updatedConfig: RsbuildConfig = {
+    output: {
+      filename: {
+        js: `[name]${jsExtension}`,
+        ...config.output?.filename,
       },
     },
-    jsExtension,
+  };
+
+  const updatedJsExtension =
+    typeof updatedConfig.output?.filename?.js === 'string' &&
+    updatedConfig.output?.filename?.js
+      ? extname(updatedConfig.output.filename.js)
+      : jsExtension;
+
+  return {
+    config: updatedConfig,
+    jsExtension: updatedJsExtension,
     dtsExtension,
   };
 };
@@ -934,6 +942,7 @@ const composeBundleConfig = (
                   return callback();
                 }
               } else {
+                // TODO: add redirect.extension option
                 request = `${request}${jsExtension}`;
               }
             }
diff --git a/tests/integration/bundle-false/index.test.ts b/tests/integration/bundle-false/index.test.ts
index 32e1d7cc8..26af6c519 100644
--- a/tests/integration/bundle-false/index.test.ts
+++ b/tests/integration/bundle-false/index.test.ts
@@ -44,22 +44,44 @@ test('auto add js extension for relative import', async () => {
   const fixturePath = join(__dirname, 'js-extension');
   const { contents } = await buildAndGetResults({ fixturePath });
 
+  // basic esm
   for (const importer of [
     'import * as __WEBPACK_EXTERNAL_MODULE__bar_js__ from "./bar.js";',
     'import * as __WEBPACK_EXTERNAL_MODULE__baz_js__ from "./baz.js";',
     'import * as __WEBPACK_EXTERNAL_MODULE__foo_js__ from "./foo.js";',
     'import * as __WEBPACK_EXTERNAL_MODULE__qux_js__ from "./qux.js";',
   ]) {
-    expect(Object.values(contents.esm)[3]).toContain(importer);
+    expect(Object.values(contents.esm0!)[3]).toContain(importer);
   }
 
+  // basic cjs
   for (const requirer of [
     'const external_bar_cjs_namespaceObject = require("./bar.cjs");',
     'const external_baz_cjs_namespaceObject = require("./baz.cjs");',
     'const external_foo_cjs_namespaceObject = require("./foo.cjs");',
     'const external_qux_cjs_namespaceObject = require("./qux.cjs");',
   ]) {
-    expect(Object.values(contents.cjs)[3]).toContain(requirer);
+    expect(Object.values(contents.cjs0!)[3]).toContain(requirer);
+  }
+
+  // using `autoExtension: false` along with `output.filename.js` - esm
+  for (const importer of [
+    'import * as __WEBPACK_EXTERNAL_MODULE__bar_mjs__ from "./bar.mjs";',
+    'import * as __WEBPACK_EXTERNAL_MODULE__baz_mjs__ from "./baz.mjs";',
+    'import * as __WEBPACK_EXTERNAL_MODULE__foo_mjs__ from "./foo.mjs";',
+    'import * as __WEBPACK_EXTERNAL_MODULE__qux_mjs__ from "./qux.mjs";',
+  ]) {
+    expect(Object.values(contents.esm1!)[3]).toContain(importer);
+  }
+
+  // using `autoExtension: false` along with `output.filename.js` - cjs
+  for (const requirer of [
+    'const external_bar_cjs_namespaceObject = require("./bar.cjs");',
+    'const external_baz_cjs_namespaceObject = require("./baz.cjs");',
+    'const external_foo_cjs_namespaceObject = require("./foo.cjs");',
+    'const external_qux_cjs_namespaceObject = require("./qux.cjs");',
+  ]) {
+    expect(Object.values(contents.cjs1!)[3]).toContain(requirer);
   }
 });
 
diff --git a/tests/integration/bundle-false/js-extension/rslib.config.ts b/tests/integration/bundle-false/js-extension/rslib.config.ts
index 6a10170f6..54ebfec13 100644
--- a/tests/integration/bundle-false/js-extension/rslib.config.ts
+++ b/tests/integration/bundle-false/js-extension/rslib.config.ts
@@ -5,9 +5,43 @@ export default defineConfig({
   lib: [
     generateBundleEsmConfig({
       bundle: false,
+      output: {
+        distPath: {
+          root: './dist/basic-esm',
+        },
+      },
     }),
     generateBundleCjsConfig({
       bundle: false,
+      output: {
+        distPath: {
+          root: './dist/basic-cjs',
+        },
+      },
+    }),
+    generateBundleEsmConfig({
+      bundle: false,
+      output: {
+        distPath: {
+          root: './dist/no-auto-extension-esm',
+        },
+        filename: {
+          js: '[name].mjs',
+        },
+      },
+      autoExtension: false,
+    }),
+    generateBundleCjsConfig({
+      bundle: false,
+      output: {
+        distPath: {
+          root: './dist/no-auto-extension-cjs',
+        },
+        filename: {
+          js: '[name].cjs',
+        },
+      },
+      autoExtension: false,
     }),
   ],
   source: {