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..f5a7bdbc4e60 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
@@ -18,6 +18,7 @@
 
 import java.io.IOException;
 import java.io.UncheckedIOException;
+import java.net.URI;
 import java.nio.charset.Charset;
 import java.util.ArrayList;
 import java.util.Collection;
@@ -46,6 +47,7 @@
  * {@link PathMatchingResourcePatternResolver} to find migration files in a native image.
  *
  * @author Moritz Halbritter
+ * @author Dongliang Xie
  */
 class NativeImageResourceProvider implements ResourceProvider {
 
@@ -106,9 +108,8 @@ 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 +141,60 @@ 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(location, root, resource)));
 			}
 		}
 	}
 
+	private String getClassPathResourcePath(Location location, Resource root, Resource resource) {
+		if (resource instanceof org.springframework.core.io.ClassPathResource classPathResource) {
+			return classPathResource.getPath();
+		}
+		String rootPath = location.getRootPath();
+		String resourcePath = getResourcePathRelativeToRoot(root, resource, rootPath);
+		return (rootPath.isEmpty()) ? resourcePath : rootPath + "/" + resourcePath;
+	}
+
+	private String getResourcePathRelativeToRoot(Resource root, Resource resource, String rootPath) {
+		try {
+			URI rootUri = root.getURI();
+			URI resourceUri = resource.getURI();
+			String relativePath = getRelativePath(rootUri, resourceUri);
+			if (relativePath != null) {
+				return relativePath;
+			}
+			String path = getUriPath(resourceUri);
+			if (!rootPath.isEmpty()) {
+				int rootPathIndex = path.indexOf(rootPath + "/");
+				if (rootPathIndex != -1) {
+					return path.substring(rootPathIndex + rootPath.length() + 1);
+				}
+			}
+			String filename = resource.getFilename();
+			return (filename != null) ? filename : path;
+		}
+		catch (IOException ex) {
+			throw new UncheckedIOException("Failed to determine path for " + resource, ex);
+		}
+	}
+
+	private @Nullable String getRelativePath(URI rootUri, URI resourceUri) {
+		String rootPath = asDirectoryPath(rootUri);
+		String resourcePath = getUriPath(resourceUri);
+		return (resourcePath.startsWith(rootPath)) ? resourcePath.substring(rootPath.length()) : null;
+	}
+
+	private String asDirectoryPath(URI uri) {
+		String path = getUriPath(uri);
+		return (path.endsWith("/")) ? path : path + "/";
+	}
+
+	private String getUriPath(URI uri) {
+		String path = uri.getPath();
+		return (path != null) ? path : uri.toString();
+	}
+
 	private Resource[] getResources(PathMatchingResourcePatternResolver resolver, Location location, Resource root) {
 		try {
 			return resolver.getResources(root.getURI() + "/**/*");
@@ -154,7 +204,7 @@ 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/NativeImageResourceProviderCustomizerTests.java b/module/spring-boot-flyway/src/test/java/org/springframework/boot/flyway/autoconfigure/NativeImageResourceProviderCustomizerTests.java
index 541f2d0215bb..9c2ac033b3fb 100644
--- a/module/spring-boot-flyway/src/test/java/org/springframework/boot/flyway/autoconfigure/NativeImageResourceProviderCustomizerTests.java
+++ b/module/spring-boot-flyway/src/test/java/org/springframework/boot/flyway/autoconfigure/NativeImageResourceProviderCustomizerTests.java
@@ -16,23 +16,34 @@
 
 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.configuration.FluentConfiguration;
 import org.flywaydb.core.api.resource.LoadableResource;
 import org.flywaydb.core.internal.resource.NoopResourceProvider;
+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.boot.testsupport.classpath.resources.WithResources;
+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 NativeImageResourceProviderCustomizer}.
  *
  * @author Moritz Halbritter
+ * @author Dongliang Xie
  */
 class NativeImageResourceProviderCustomizerTests {
 
@@ -70,6 +81,29 @@ void nativeImageResourceProviderShouldFindNestedMigrations() {
 		assertThat(migrations).containsExactlyInAnyOrder(v1, v2);
 	}
 
+	@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 {
+			@SuppressWarnings("unchecked")
+			Scanner<Object> scanner = mock(Scanner.class);
+			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");
+		}
+	}
+
 	@Test
 	void shouldBackOffOnCustomResourceProvider() {
 		FluentConfiguration configuration = new FluentConfiguration();