diff --git a/module/spring-boot-flyway/src/main/java/org/springframework/boot/flyway/autoconfigure/NativeImageResourceProvider.java b/module/spring-boot-flyway/src/main/java/org/springframework/boot/flyway/autoconfigure/NativeImageResourceProvider.java
index d5065b9f689f..51dbf9e84412 100644
--- a/module/spring-boot-flyway/src/main/java/org/springframework/boot/flyway/autoconfigure/NativeImageResourceProvider.java
+++ b/module/spring-boot-flyway/src/main/java/org/springframework/boot/flyway/autoconfigure/NativeImageResourceProvider.java
@@ -38,6 +38,7 @@
 import org.springframework.core.NativeDetector;
 import org.springframework.core.io.Resource;
 import org.springframework.core.io.support.PathMatchingResourcePatternResolver;
+import org.springframework.util.PathMatcher;
 
 /**
  * A Flyway {@link ResourceProvider} which supports GraalVM native-image.
@@ -46,6 +47,8 @@
  * {@link PathMatchingResourcePatternResolver} to find migration files in a native image.
  *
  * @author Moritz Halbritter
+ * @author Dongliang Xie
+ * @author Stephane Nicoll
  */
 class NativeImageResourceProvider implements ResourceProvider {
 
@@ -106,9 +109,8 @@ public Collection<LoadableResource> getResources(String prefix, String[] suffixe
 	}
 
 	private ClassPathResource asClassPathResource(LocatedResource locatedResource) {
-		Location location = locatedResource.location();
-		String fileNameWithAbsolutePath = location.getRootPath() + "/" + locatedResource.resource().getFilename();
-		return new ClassPathResource(location, fileNameWithAbsolutePath, this.classLoader, this.encoding);
+		return new ClassPathResource(locatedResource.location(), locatedResource.path(), this.classLoader,
+				this.encoding);
 	}
 
 	private void ensureInitialized() {
@@ -140,11 +142,28 @@ private void initialize() {
 			}
 			Resource[] resources = getResources(resolver, location, root);
 			for (Resource resource : resources) {
-				this.locatedResources.add(new LocatedResource(resource, location));
+				this.locatedResources.add(new LocatedResource(resource, location,
+						getClassPathResourcePath(resolver.getPathMatcher(), location, root, resource)));
 			}
 		}
 	}
 
+	private String getClassPathResourcePath(PathMatcher pathMatcher, Location location, Resource root,
+			Resource resource) {
+		if (resource instanceof org.springframework.core.io.ClassPathResource classPathResource) {
+			return classPathResource.getPath();
+		}
+		try {
+			String rootPath = location.getRootPath();
+			String relativePath = pathMatcher.extractPathWithinPattern(root.getURI() + "/**/*",
+					resource.getURI().toString());
+			return (rootPath.isEmpty()) ? relativePath : rootPath + "/" + relativePath;
+		}
+		catch (IOException ex) {
+			throw new UncheckedIOException("Failed to determine path for " + resource, ex);
+		}
+	}
+
 	private Resource[] getResources(PathMatchingResourcePatternResolver resolver, Location location, Resource root) {
 		try {
 			return resolver.getResources(root.getURI() + "/**/*");
@@ -154,7 +173,7 @@ private Resource[] getResources(PathMatchingResourcePatternResolver resolver, Lo
 		}
 	}
 
-	private record LocatedResource(Resource resource, Location location) {
+	private record LocatedResource(Resource resource, Location location, String path) {
 
 	}
 
diff --git a/module/spring-boot-flyway/src/test/java/org/springframework/boot/flyway/autoconfigure/NativeImageResourceProviderTests.java b/module/spring-boot-flyway/src/test/java/org/springframework/boot/flyway/autoconfigure/NativeImageResourceProviderTests.java
new file mode 100644
index 000000000000..4fd5853e93be
--- /dev/null
+++ b/module/spring-boot-flyway/src/test/java/org/springframework/boot/flyway/autoconfigure/NativeImageResourceProviderTests.java
@@ -0,0 +1,69 @@
+/*
+ * Copyright 2012-present the original author or authors.
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *      https://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package org.springframework.boot.flyway.autoconfigure;
+
+import java.io.IOException;
+import java.nio.charset.StandardCharsets;
+import java.util.Collection;
+import java.util.Collections;
+import java.util.List;
+
+import org.flywaydb.core.api.Location;
+import org.flywaydb.core.api.ResourceProvider;
+import org.flywaydb.core.api.resource.LoadableResource;
+import org.flywaydb.core.internal.scanner.Scanner;
+import org.junit.jupiter.api.Test;
+
+import org.springframework.boot.testsupport.classpath.ForkedClassPath;
+import org.springframework.boot.testsupport.classpath.resources.WithResource;
+import org.springframework.util.FileCopyUtils;
+
+import static org.assertj.core.api.Assertions.assertThat;
+import static org.mockito.BDDMockito.given;
+import static org.mockito.Mockito.mock;
+
+/**
+ * Tests for {@link NativeImageResourceProvider}.
+ *
+ * @author Dongliang Xie
+ * @author Stephane Nicoll
+ */
+class NativeImageResourceProviderTests {
+
+	@Test
+	@ForkedClassPath
+	@WithResource(name = "db/migration/nested/V2__users.sql", content = "select 1;")
+	void nativeImageResourceProviderShouldReadNestedMigrations() throws IOException {
+		System.setProperty("org.graalvm.nativeimage.imagecode", "true");
+		try {
+			Scanner<?> scanner = mock();
+			given(scanner.getResources("V", ".sql")).willReturn(Collections.emptyList());
+			Location location = Location.fromPath("classpath:", "db/migration");
+			ClassLoader classLoader = Thread.currentThread().getContextClassLoader();
+			ResourceProvider resourceProvider = new NativeImageResourceProvider(scanner, classLoader, List.of(location),
+					StandardCharsets.UTF_8, true);
+			Collection<LoadableResource> migrations = resourceProvider.getResources("V", new String[] { ".sql" });
+			assertThat(migrations).hasSize(1);
+			LoadableResource migration = migrations.iterator().next();
+			assertThat(FileCopyUtils.copyToString(migration.read())).isEqualTo("select 1;");
+		}
+		finally {
+			System.clearProperty("org.graalvm.nativeimage.imagecode");
+		}
+	}
+
+}