diff --git a/docs/sql-migration-guide-upgrade.md b/docs/sql-migration-guide-upgrade.md
index 55838e773e4b..e48125a0972b 100644
--- a/docs/sql-migration-guide-upgrade.md
+++ b/docs/sql-migration-guide-upgrade.md
@@ -29,6 +29,8 @@ displayTitle: Spark SQL Upgrading Guide
 
   - In Spark version 2.4 and earlier, users can create a map with duplicated keys via built-in functions like `CreateMap`, `StringToMap`, etc. The behavior of map with duplicated keys is undefined, e.g. map look up respects the duplicated key appears first, `Dataset.collect` only keeps the duplicated key appears last, `MapKeys` returns duplicated keys, etc. Since Spark 3.0, these built-in functions will remove duplicated map keys with last wins policy. Users may still read map values with duplicated keys from data sources which do not enforce it (e.g. Parquet), the behavior will be udefined.
 
+  - In Spark version 2.4 and earlier, the `SET` command works without any warnings even if the specified key is for `SparkConf` entries and it has no effect because the command does not update `SparkConf`, but the behavior might confuse users. Since 3.0, the command fails if a `SparkConf` key is used. You can disable such a check by setting `spark.sql.legacy.execution.setCommandRejectsSparkConfs` to `false`.
+
 ## Upgrading From Spark SQL 2.3 to 2.4
 
   - In Spark version 2.3 and earlier, the second parameter to array_contains function is implicitly promoted to the element type of first array type parameter. This type promotion can be lossy and may cause `array_contains` function to return wrong result. This problem has been addressed in 2.4 by employing a safer type promotion mechanism. This can cause some change in behavior and are illustrated in the table below.
diff --git a/sql/catalyst/src/main/scala/org/apache/spark/sql/internal/SQLConf.scala b/sql/catalyst/src/main/scala/org/apache/spark/sql/internal/SQLConf.scala
index 7bcf21595ce5..f1c845bc9450 100644
--- a/sql/catalyst/src/main/scala/org/apache/spark/sql/internal/SQLConf.scala
+++ b/sql/catalyst/src/main/scala/org/apache/spark/sql/internal/SQLConf.scala
@@ -45,7 +45,7 @@ import org.apache.spark.util.Utils
 
 object SQLConf {
 
-  private val sqlConfEntries = java.util.Collections.synchronizedMap(
+  private[sql] val sqlConfEntries = java.util.Collections.synchronizedMap(
     new java.util.HashMap[String, ConfigEntry[_]]())
 
   val staticConfKeys: java.util.Set[String] =
@@ -1610,6 +1610,14 @@ object SQLConf {
       """ "... N more fields" placeholder.""")
     .intConf
     .createWithDefault(25)
+
+  val SET_COMMAND_REJECTS_SPARK_CONFS =
+    buildConf("spark.sql.legacy.execution.setCommandRejectsSparkConfs")
+      .internal()
+      .doc("If it is set to true, SET command will fail when the key is registered as " +
+        "a SparkConf entry.")
+      .booleanConf
+      .createWithDefault(true)
 }
 
 /**
@@ -2030,6 +2038,8 @@ class SQLConf extends Serializable with Logging {
 
   def maxToStringFields: Int = getConf(SQLConf.MAX_TO_STRING_FIELDS)
 
+  def setCommandRejectsSparkConfs: Boolean = getConf(SQLConf.SET_COMMAND_REJECTS_SPARK_CONFS)
+
   /** ********************** SQLConf functionality methods ************ */
 
   /** Set Spark SQL configuration properties. */
diff --git a/sql/core/src/main/scala/org/apache/spark/sql/RuntimeConfig.scala b/sql/core/src/main/scala/org/apache/spark/sql/RuntimeConfig.scala
index 5a554eff02e3..d83a01ff9ea6 100644
--- a/sql/core/src/main/scala/org/apache/spark/sql/RuntimeConfig.scala
+++ b/sql/core/src/main/scala/org/apache/spark/sql/RuntimeConfig.scala
@@ -153,5 +153,9 @@ class RuntimeConfig private[sql](sqlConf: SQLConf = new SQLConf) {
     if (SQLConf.staticConfKeys.contains(key)) {
       throw new AnalysisException(s"Cannot modify the value of a static config: $key")
     }
+    if (sqlConf.setCommandRejectsSparkConfs &&
+        ConfigEntry.findEntry(key) != null && !SQLConf.sqlConfEntries.containsKey(key)) {
+      throw new AnalysisException(s"Cannot modify the value of a Spark config: $key")
+    }
   }
 }
diff --git a/sql/core/src/test/scala/org/apache/spark/sql/RuntimeConfigSuite.scala b/sql/core/src/test/scala/org/apache/spark/sql/RuntimeConfigSuite.scala
index cdcea09ad975..6196757eb701 100644
--- a/sql/core/src/test/scala/org/apache/spark/sql/RuntimeConfigSuite.scala
+++ b/sql/core/src/test/scala/org/apache/spark/sql/RuntimeConfigSuite.scala
@@ -18,6 +18,7 @@
 package org.apache.spark.sql
 
 import org.apache.spark.SparkFunSuite
+import org.apache.spark.internal.config
 
 class RuntimeConfigSuite extends SparkFunSuite {
 
@@ -68,4 +69,13 @@ class RuntimeConfigSuite extends SparkFunSuite {
     assert(!conf.isModifiable(""))
     assert(!conf.isModifiable("invalid config parameter"))
   }
+
+  test("reject SparkConf entries") {
+    val conf = newConf()
+
+    val ex = intercept[AnalysisException] {
+      conf.set(config.CPUS_PER_TASK.key, 4)
+    }
+    assert(ex.getMessage.contains("Spark config"))
+  }
 }
diff --git a/sql/core/src/test/scala/org/apache/spark/sql/execution/command/DDLSuite.scala b/sql/core/src/test/scala/org/apache/spark/sql/execution/command/DDLSuite.scala
index f8d98dead2d4..9d32fb6d4696 100644
--- a/sql/core/src/test/scala/org/apache/spark/sql/execution/command/DDLSuite.scala
+++ b/sql/core/src/test/scala/org/apache/spark/sql/execution/command/DDLSuite.scala
@@ -24,6 +24,7 @@ import java.util.Locale
 import org.apache.hadoop.fs.Path
 import org.scalatest.BeforeAndAfterEach
 
+import org.apache.spark.internal.config
 import org.apache.spark.sql.{AnalysisException, QueryTest, Row, SaveMode}
 import org.apache.spark.sql.catalyst.TableIdentifier
 import org.apache.spark.sql.catalyst.analysis.{FunctionRegistry, NoSuchPartitionException, NoSuchTableException, TempTableAlreadyExistsException}
@@ -2715,4 +2716,11 @@ abstract class DDLSuite extends QueryTest with SQLTestUtils {
       }
     }
   }
+
+  test("set command rejects SparkConf entries") {
+    val ex = intercept[AnalysisException] {
+      sql(s"SET ${config.CPUS_PER_TASK.key} = 4")
+    }
+    assert(ex.getMessage.contains("Spark config"))
+  }
 }