diff --git a/sql/catalyst/src/main/scala/org/apache/spark/sql/catalyst/optimizer/NestedColumnAliasing.scala b/sql/catalyst/src/main/scala/org/apache/spark/sql/catalyst/optimizer/NestedColumnAliasing.scala
index 977e9b1ab1329..b8ab8b78ccbc2 100644
--- a/sql/catalyst/src/main/scala/org/apache/spark/sql/catalyst/optimizer/NestedColumnAliasing.scala
+++ b/sql/catalyst/src/main/scala/org/apache/spark/sql/catalyst/optimizer/NestedColumnAliasing.scala
@@ -184,9 +184,20 @@ object NestedColumnAliasing {
       plan: LogicalPlan,
       nestedFieldToAlias: Map[Expression, Alias],
       attrToAliases: AttributeMap[Seq[Alias]]): LogicalPlan = {
-    plan.withNewChildren(plan.children.map { plan =>
-      Project(plan.output.flatMap(a => attrToAliases.getOrElse(a, Seq(a))), plan)
-    }).transformExpressions {
+    val newChildPlan = plan match {
+      case g: Generate =>
+        g.withNewChildren(g.children.map { childPlan =>
+          val origOutput = childPlan.output
+          val fromAlias = childPlan.output.flatMap(a => attrToAliases.getOrElse(a, Nil))
+          Project(origOutput ++ fromAlias, childPlan)
+        })
+      case p =>
+        p.withNewChildren(p.children.map { childPlan =>
+          Project(childPlan.output.flatMap(a => attrToAliases.getOrElse(a, Seq(a))), childPlan)
+        })
+    }
+
+    newChildPlan.transformExpressions {
       case f: ExtractValue if nestedFieldToAlias.contains(f.canonicalized) =>
         nestedFieldToAlias(f.canonicalized).toAttribute
     }
diff --git a/sql/core/src/test/scala/org/apache/spark/sql/execution/SparkPlanSuite.scala b/sql/core/src/test/scala/org/apache/spark/sql/execution/SparkPlanSuite.scala
index 12d311d6835b7..d91da0488cdbc 100644
--- a/sql/core/src/test/scala/org/apache/spark/sql/execution/SparkPlanSuite.scala
+++ b/sql/core/src/test/scala/org/apache/spark/sql/execution/SparkPlanSuite.scala
@@ -143,6 +143,48 @@ class SparkPlanSuite extends QueryTest with SharedSparkSession {
       }
     }
   }
+
+  test("SPARK-39854: replaceWithAliases should keep the order of Generate children") {
+    import org.apache.spark.sql.functions.{explode, struct}
+    import org.apache.spark.sql.SparkSession
+    val ss: SparkSession = spark
+    import ss.implicits._
+    val testJson =
+      """{
+        | "b": {
+        |  "id": "id00",
+        |  "data": [{
+        |   "b1": "vb1",
+        |   "b2": 101,
+        |   "ex2": [
+        |    { "fb1": false, "fb2": 11, "fb3": "t1" },
+        |    { "fb1": true, "fb2": 12, "fb3": "t2" }
+        |   ]}, {
+        |   "b1": "vb2",
+        |   "b2": 102,
+        |   "ex2": [
+        |    { "fb1": false, "fb2": 13, "fb3": "t3" },
+        |    { "fb1": true, "fb2": 14, "fb3": "t4" }
+        |   ]}
+        |  ],
+        |  "fa": "tes",
+        |  "v": "1.5"
+        | }
+        |}
+        |""".stripMargin
+    val df = spark.read.json((testJson :: Nil).toDS())
+      .withColumn("ex_b", explode($"b.data.ex2"))
+      .withColumn("ex_b2", explode($"ex_b"))
+    val df1 = df
+      .withColumn("rt", struct(
+        $"b.fa".alias("rt_fa"),
+        $"b.v".alias("rt_v")
+      ))
+      .drop("b", "ex_b")
+
+    val result = df1.collect()
+    assert(result.length == 4)
+  }
 }
 
 case class ColumnarOp(child: SparkPlan) extends UnaryExecNode {