diff --git a/spark/src/main/scala/org/apache/comet/CometSparkSessionExtensions.scala b/spark/src/main/scala/org/apache/comet/CometSparkSessionExtensions.scala
index 8ef8cb83e8..d3f197cc75 100644
--- a/spark/src/main/scala/org/apache/comet/CometSparkSessionExtensions.scala
+++ b/spark/src/main/scala/org/apache/comet/CometSparkSessionExtensions.scala
@@ -741,9 +741,32 @@ class CometSparkSessionExtensions
         }
 
         // Set up logical links
-        newPlan = newPlan.transform { case op: CometExec =>
-          op.originalPlan.logicalLink.foreach(op.setLogicalLink)
-          op
+        newPlan = newPlan.transform {
+          case op: CometExec =>
+            op.originalPlan.logicalLink.foreach(op.setLogicalLink)
+            op
+          case op: CometShuffleExchangeExec =>
+            // Original Spark shuffle exchange operator might have empty logical link.
+            // But the `setLogicalLink` call above on downstream operator of
+            // `CometShuffleExchangeExec` will set its logical link to the downstream
+            // operators which cause AQE behavior to be incorrect. So we need to unset
+            // the logical link here.
+            if (op.originalPlan.logicalLink.isEmpty) {
+              op.unsetTagValue(SparkPlan.LOGICAL_PLAN_TAG)
+              op.unsetTagValue(SparkPlan.LOGICAL_PLAN_INHERITED_TAG)
+            } else {
+              op.originalPlan.logicalLink.foreach(op.setLogicalLink)
+            }
+            op
+
+          case op: CometBroadcastExchangeExec =>
+            if (op.originalPlan.logicalLink.isEmpty) {
+              op.unsetTagValue(SparkPlan.LOGICAL_PLAN_TAG)
+              op.unsetTagValue(SparkPlan.LOGICAL_PLAN_INHERITED_TAG)
+            } else {
+              op.originalPlan.logicalLink.foreach(op.setLogicalLink)
+            }
+            op
         }
 
         // Convert native execution block by linking consecutive native operators.
diff --git a/spark/src/main/scala/org/apache/spark/sql/comet/execution/shuffle/CometShuffleExchangeExec.scala b/spark/src/main/scala/org/apache/spark/sql/comet/execution/shuffle/CometShuffleExchangeExec.scala
index 232b6bf17f..faa52cd06b 100644
--- a/spark/src/main/scala/org/apache/spark/sql/comet/execution/shuffle/CometShuffleExchangeExec.scala
+++ b/spark/src/main/scala/org/apache/spark/sql/comet/execution/shuffle/CometShuffleExchangeExec.scala
@@ -61,6 +61,7 @@ import org.apache.comet.shims.ShimCometShuffleExchangeExec
 case class CometShuffleExchangeExec(
     override val outputPartitioning: Partitioning,
     child: SparkPlan,
+    originalPlan: ShuffleExchangeLike,
     shuffleOrigin: ShuffleOrigin = ENSURE_REQUIREMENTS,
     shuffleType: ShuffleType = CometNativeShuffle,
     advisoryPartitionSize: Option[Long] = None)
diff --git a/spark/src/main/spark-3.x/org/apache/comet/shims/ShimCometShuffleExchangeExec.scala b/spark/src/main/spark-3.x/org/apache/comet/shims/ShimCometShuffleExchangeExec.scala
index f89dbb8dba..6b4fad974f 100644
--- a/spark/src/main/spark-3.x/org/apache/comet/shims/ShimCometShuffleExchangeExec.scala
+++ b/spark/src/main/spark-3.x/org/apache/comet/shims/ShimCometShuffleExchangeExec.scala
@@ -32,6 +32,7 @@ trait ShimCometShuffleExchangeExec {
     CometShuffleExchangeExec(
       s.outputPartitioning,
       s.child,
+      s,
       s.shuffleOrigin,
       shuffleType,
       advisoryPartitionSize)
diff --git a/spark/src/test/scala/org/apache/comet/exec/CometExecSuite.scala b/spark/src/test/scala/org/apache/comet/exec/CometExecSuite.scala
index e5b3523dcf..5e86757f64 100644
--- a/spark/src/test/scala/org/apache/comet/exec/CometExecSuite.scala
+++ b/spark/src/test/scala/org/apache/comet/exec/CometExecSuite.scala
@@ -38,7 +38,7 @@ import org.apache.spark.sql.catalyst.expressions.aggregate.AggregateMode
 import org.apache.spark.sql.comet.{CometBroadcastExchangeExec, CometCollectLimitExec, CometFilterExec, CometHashAggregateExec, CometHashJoinExec, CometProjectExec, CometRowToColumnarExec, CometScanExec, CometSortExec, CometSortMergeJoinExec, CometTakeOrderedAndProjectExec}
 import org.apache.spark.sql.comet.execution.shuffle.{CometColumnarShuffle, CometShuffleExchangeExec}
 import org.apache.spark.sql.execution.{CollectLimitExec, ProjectExec, SQLExecution, UnionExec}
-import org.apache.spark.sql.execution.exchange.BroadcastExchangeExec
+import org.apache.spark.sql.execution.exchange.{BroadcastExchangeExec, ShuffleExchangeExec}
 import org.apache.spark.sql.execution.joins.{BroadcastNestedLoopJoinExec, CartesianProductExec, SortMergeJoinExec}
 import org.apache.spark.sql.execution.window.WindowExec
 import org.apache.spark.sql.expressions.Window
@@ -62,6 +62,37 @@ class CometExecSuite extends CometTestBase {
     }
   }
 
+  test("CometShuffleExchangeExec logical link should be correct") {
+    withTempView("v") {
+      spark.sparkContext
+        .parallelize((1 to 4).map(i => TestData(i, i.toString)), 2)
+        .toDF("c1", "c2")
+        .createOrReplaceTempView("v")
+
+      withSQLConf(
+        SQLConf.ADAPTIVE_EXECUTION_ENABLED.key -> "false",
+        CometConf.COMET_COLUMNAR_SHUFFLE_ENABLED.key -> "true") {
+        val df = sql("SELECT * FROM v where c1 = 1 order by c1, c2")
+        val shuffle = find(df.queryExecution.executedPlan) {
+          case _: CometShuffleExchangeExec => true
+          case _ => false
+        }.get.asInstanceOf[CometShuffleExchangeExec]
+        assert(shuffle.logicalLink.isEmpty)
+      }
+
+      withSQLConf(
+        SQLConf.ADAPTIVE_EXECUTION_ENABLED.key -> "false",
+        CometConf.COMET_COLUMNAR_SHUFFLE_ENABLED.key -> "false") {
+        val df = sql("SELECT * FROM v where c1 = 1 order by c1, c2")
+        val shuffle = find(df.queryExecution.executedPlan) {
+          case _: ShuffleExchangeExec => true
+          case _ => false
+        }.get.asInstanceOf[ShuffleExchangeExec]
+        assert(shuffle.logicalLink.isEmpty)
+      }
+    }
+  }
+
   test("Ensure that the correct outputPartitioning of CometSort") {
     withTable("test_data") {
       val tableDF = spark.sparkContext
@@ -302,7 +333,8 @@ class CometExecSuite extends CometTestBase {
     withSQLConf(
       CometConf.COMET_EXEC_ENABLED.key -> "true",
       CometConf.COMET_EXEC_ALL_OPERATOR_ENABLED.key -> "true",
-      "spark.sql.autoBroadcastJoinThreshold" -> "0",
+      "spark.sql.adaptive.autoBroadcastJoinThreshold" -> "-1",
+      "spark.sql.autoBroadcastJoinThreshold" -> "-1",
       "spark.sql.join.preferSortMergeJoin" -> "true") {
       withParquetTable((0 until 5).map(i => (i, i + 1)), "tbl1") {
         withParquetTable((0 until 5).map(i => (i, i + 1)), "tbl2") {
@@ -1306,3 +1338,5 @@ case class BucketedTableTestSpec(
     expectedShuffle: Boolean = true,
     expectedSort: Boolean = true,
     expectedNumOutputPartitions: Option[Int] = None)
+
+case class TestData(key: Int, value: String)