diff --git a/packages/rstack/src/rsbuildConfig.ts b/packages/rstack/src/rsbuildConfig.ts
index 466d470..a6ef3cc 100644
--- a/packages/rstack/src/rsbuildConfig.ts
+++ b/packages/rstack/src/rsbuildConfig.ts
@@ -1,21 +1,26 @@
-import type { ConfigParams, RsbuildConfigDefinition } from '@rsbuild/core';
+import {
+  type ConfigParams,
+  type RsbuildConfig,
+  type RsbuildConfigDefinition,
+  mergeRsbuildConfig,
+} from '@rsbuild/core';
 import { withConfigMeta } from '@rstackjs/load-config';
 import { loadRstackConfig, type Configs } from './config.ts';
+import { resolveConfigLayers } from './configLayers.ts';
 
-const resolveRsbuildConfig = async (configs: Configs, params: ConfigParams) => {
-  const appConfig = configs.app;
-  if (!appConfig) {
-    return {};
-  }
-  if (typeof appConfig === 'function') {
-    return appConfig(params);
-  }
-  return appConfig;
+export const resolveRsbuildConfig = async (
+  layers: readonly Configs[],
+  params: ConfigParams,
+): Promise<RsbuildConfig> => {
+  const configs = await resolveConfigLayers(layers, 'app', params);
+  return configs.length > 1
+    ? mergeRsbuildConfig(...configs)
+    : (configs[0] ?? {});
 };
 
 const loadRsbuildConfig: RsbuildConfigDefinition = async (params) => {
   const { configs, filePath, dependencies } = await loadRstackConfig();
-  const config = await resolveRsbuildConfig(configs, params);
+  const config = await resolveRsbuildConfig([configs], params);
 
   return withConfigMeta(config, { filePath, dependencies });
 };
diff --git a/packages/rstack/tests/config/app-merge.test.ts b/packages/rstack/tests/config/app-merge.test.ts
new file mode 100644
index 0000000..2f1292c
--- /dev/null
+++ b/packages/rstack/tests/config/app-merge.test.ts
@@ -0,0 +1,31 @@
+import { expect, test } from 'rstack/test';
+import { resolveRsbuildConfig } from '../../src/rsbuildConfig.ts';
+
+test('merges app layers using native Rsbuild rules', async () => {
+  const config = await resolveRsbuildConfig(
+    [
+      {
+        app: {
+          source: {
+            define: { SHARED: true, ENV: 'base' },
+            preEntry: ['./base.ts'],
+          },
+        },
+      },
+      {
+        app: {
+          source: {
+            define: { ENV: 'production' },
+            preEntry: ['./project.ts'],
+          },
+        },
+      },
+    ],
+    { command: 'build', env: 'production' },
+  );
+
+  expect(config.source).toEqual({
+    define: { SHARED: true, ENV: 'production' },
+    preEntry: ['./base.ts', './project.ts'],
+  });
+});