diff --git a/backends-clickhouse/src/test/scala/org/apache/gluten/execution/GlutenFunctionValidateSuite.scala b/backends-clickhouse/src/test/scala/org/apache/gluten/execution/GlutenFunctionValidateSuite.scala
index 6a0196e2b18..40c5ab10bbb 100644
--- a/backends-clickhouse/src/test/scala/org/apache/gluten/execution/GlutenFunctionValidateSuite.scala
+++ b/backends-clickhouse/src/test/scala/org/apache/gluten/execution/GlutenFunctionValidateSuite.scala
@@ -668,6 +668,22 @@ class GlutenFunctionValidateSuite extends GlutenClickHouseWholeStageTransformerS
     }
   }
 
+  test("test flatten with nullable inner arrays") {
+    val sql =
+      """
+        |select id, flatten(arr)
+        |from (
+        |  select id,
+        |    if(id = 0,
+        |      array(array(cast(id + 1 as int)), cast(null as array<int>)),
+        |      array(array(cast(id + 1 as int)))) as arr
+        |  from range(2)
+        |)
+        |order by id
+        |""".stripMargin
+    runQueryAndCompare(sql)(checkGlutenPlan[ProjectExecTransformer])
+  }
+
   test("test common subexpression eliminate") {
     def checkOperatorCount[T <: TransformSupport](count: Int)(df: DataFrame)(implicit
         tag: ClassTag[T]): Unit = {
diff --git a/cpp-ch/local-engine/Functions/SparkArrayFlatten.cpp b/cpp-ch/local-engine/Functions/SparkArrayFlatten.cpp
index 96faa9d1dc1..7ead48cac1f 100644
--- a/cpp-ch/local-engine/Functions/SparkArrayFlatten.cpp
+++ b/cpp-ch/local-engine/Functions/SparkArrayFlatten.cpp
@@ -16,6 +16,7 @@
  */
 #include <Columns/ColumnArray.h>
 #include <Columns/ColumnNullable.h>
+#include <Columns/ColumnVector.h>
 #include <DataTypes/DataTypeArray.h>
 #include <DataTypes/DataTypeNullable.h>
 #include <Functions/FunctionFactory.h>
@@ -107,19 +108,27 @@ result: Row 1: [1, 2, 3], Row2: [4]
         const IColumn::Offsets * prev_offsets = &src_offsets;
         const IColumn * prev_data = &src_col->getData();
         bool nullable = prev_data->isNullable();
-        // when array has null element, return null
+        ColumnUInt8::MutablePtr result_null_map;
+        // When an inner array is null, only the corresponding outer row is null.
         if (nullable)
         {
             const ColumnNullable *  nullable_column = checkAndGetColumn<ColumnNullable>(prev_data);
             prev_data = nullable_column->getNestedColumnPtr().get();
-            for (size_t i = 0; i < nullable_column->size(); i++)
+            result_null_map = ColumnUInt8::create(input_rows_count, 0);
+            auto & result_null_map_data = result_null_map->getData();
+            size_t prev_offset = 0;
+            for (size_t row = 0; row < input_rows_count; ++row)
             {
-                if (nullable_column->isNullAt(i))
+                const auto current_offset = src_offsets[row];
+                for (size_t i = prev_offset; i < current_offset; ++i)
                 {
-                    auto res= nullable_column->cloneEmpty();
-                    res->insertManyDefaults(input_rows_count);
-                    return res;
+                    if (nullable_column->isNullAt(i))
+                    {
+                        result_null_map_data[row] = 1;
+                        break;
+                    }
                 }
+                prev_offset = current_offset;
             }
         }
         if (isNothing(prev_data->getDataType()))
@@ -142,7 +151,7 @@ result: Row 1: [1, 2, 3], Row2: [4]
             prev_data->getPtr(),
             result_offsets_column ? std::move(result_offsets_column) : src_col->getOffsetsPtr());
         if (nullable)
-            return  makeNullable(res);
+            return ColumnNullable::create(std::move(res), std::move(result_null_map));
         return res;
     }