diff --git a/sql/core/src/main/scala/org/apache/spark/sql/execution/datasources/PartitioningAwareFileIndex.scala b/sql/core/src/main/scala/org/apache/spark/sql/execution/datasources/PartitioningAwareFileIndex.scala
index 3adec2f79073..7bfe42931f4a 100644
--- a/sql/core/src/main/scala/org/apache/spark/sql/execution/datasources/PartitioningAwareFileIndex.scala
+++ b/sql/core/src/main/scala/org/apache/spark/sql/execution/datasources/PartitioningAwareFileIndex.scala
@@ -221,7 +221,15 @@ abstract class PartitioningAwareFileIndex(
         if (!fs.isDirectory(userDefinedBasePath)) {
           throw new IllegalArgumentException(s"Option '$BASE_PATH_PARAM' must be a directory")
         }
-        Set(fs.makeQualified(userDefinedBasePath))
+        val qualifiedBasePath = fs.makeQualified(userDefinedBasePath)
+        val qualifiedBasePathStr = qualifiedBasePath.toString
+        rootPaths
+          .find(!fs.makeQualified(_).toString.startsWith(qualifiedBasePathStr))
+          .foreach { rp =>
+            throw new IllegalArgumentException(
+              s"Wrong basePath $userDefinedBasePath for the root path: $rp")
+          }
+        Set(qualifiedBasePath)
 
       case None =>
         rootPaths.map { path =>
diff --git a/sql/core/src/test/scala/org/apache/spark/sql/execution/datasources/FileIndexSuite.scala b/sql/core/src/test/scala/org/apache/spark/sql/execution/datasources/FileIndexSuite.scala
index a7a2349a1dfb..553773e2555c 100644
--- a/sql/core/src/test/scala/org/apache/spark/sql/execution/datasources/FileIndexSuite.scala
+++ b/sql/core/src/test/scala/org/apache/spark/sql/execution/datasources/FileIndexSuite.scala
@@ -352,6 +352,26 @@ class FileIndexSuite extends SharedSparkSession {
       "driver side must not be negative"))
   }
 
+  test ("SPARK-29537: throw exception when user defined a wrong base path") {
+    withTempDir { dir =>
+      val partitionDirectory = new File(dir, "a=foo")
+      partitionDirectory.mkdir()
+      val file = new File(partitionDirectory, "text.txt")
+      stringToFile(file, "text")
+      val path = new Path(dir.getCanonicalPath)
+      val wrongBasePath = new File(dir, "unknown")
+      // basePath must be a directory
+      wrongBasePath.mkdir()
+      val parameters = Map("basePath" -> wrongBasePath.getCanonicalPath)
+      val fileIndex = new InMemoryFileIndex(spark, Seq(path), parameters, None)
+      val msg = intercept[IllegalArgumentException] {
+        // trigger inferPartitioning()
+        fileIndex.partitionSpec()
+      }.getMessage
+      assert(msg === s"Wrong basePath ${wrongBasePath.getCanonicalPath} for the root path: $path")
+    }
+  }
+
   test("refresh for InMemoryFileIndex with FileStatusCache") {
     withTempDir { dir =>
       val fileStatusCache = FileStatusCache.getOrCreate(spark)
diff --git a/sql/core/src/test/scala/org/apache/spark/sql/test/DataFrameReaderWriterSuite.scala b/sql/core/src/test/scala/org/apache/spark/sql/test/DataFrameReaderWriterSuite.scala
index cef0e5ab4756..55a60940a775 100644
--- a/sql/core/src/test/scala/org/apache/spark/sql/test/DataFrameReaderWriterSuite.scala
+++ b/sql/core/src/test/scala/org/apache/spark/sql/test/DataFrameReaderWriterSuite.scala
@@ -234,6 +234,21 @@ class DataFrameReaderWriterSuite extends QueryTest with SharedSparkSession with
     assert(DataSourceUtils.decodePartitioningColumns(partColumns) === Seq("col1", "col2"))
   }
 
+  test ("SPARK-29537: throw exception when user defined a wrong base path") {
+    withTempPath { p =>
+      val path = new Path(p.toURI).toString
+      Seq((1, 1), (2, 2)).toDF("c1", "c2")
+        .write.partitionBy("c1").mode(SaveMode.Overwrite).parquet(path)
+      val wrongBasePath = new File(p, "unknown")
+      // basePath must be a directory
+      wrongBasePath.mkdir()
+      val msg = intercept[IllegalArgumentException] {
+        spark.read.option("basePath", wrongBasePath.getCanonicalPath).parquet(path)
+      }.getMessage
+      assert(msg === s"Wrong basePath ${wrongBasePath.getCanonicalPath} for the root path: $path")
+    }
+  }
+
   test("save mode") {
     spark.range(10).write
       .format("org.apache.spark.sql.test")