diff --git a/django/db/models/fields/related.py b/django/db/models/fields/related.py
index d7b61f9a5af..8cc174bdfb9 100644
--- a/django/db/models/fields/related.py
+++ b/django/db/models/fields/related.py
@@ -1228,6 +1228,15 @@ class ManyToManyField(RelatedField):
                     id='fields.W341',
                 )
             )
+        if self.remote_field.limit_choices_to and self.remote_field.through:
+            warnings.append(
+                checks.Warning(
+                    'limit_choices_to has no effect on ManyToManyField '
+                    'with a through model.',
+                    obj=self,
+                    id='fields.W343',
+                )
+            )
 
         return warnings
 
diff --git a/docs/ref/checks.txt b/docs/ref/checks.txt
index aff3bd2bdc0..5eed9f0aede 100644
--- a/docs/ref/checks.txt
+++ b/docs/ref/checks.txt
@@ -251,6 +251,8 @@ Related Fields
 * **fields.W341**: ``ManyToManyField`` does not support ``validators``.
 * **fields.W342**: Setting ``unique=True`` on a ``ForeignKey`` has the same
   effect as using a ``OneToOneField``.
+* **fields.W343**: ``limit_choices_to`` has no effect on ``ManyToManyField``
+  with a ``through`` model.
 
 Signals
 ~~~~~~~
diff --git a/tests/invalid_models_tests/test_relative_fields.py b/tests/invalid_models_tests/test_relative_fields.py
index 96d3f7815ff..f42d6a5365a 100644
--- a/tests/invalid_models_tests/test_relative_fields.py
+++ b/tests/invalid_models_tests/test_relative_fields.py
@@ -181,7 +181,18 @@ class RelativeFieldTests(SimpleTestCase):
             name = models.CharField(max_length=20)
 
         class ModelM2M(models.Model):
-            m2m = models.ManyToManyField(Model, null=True, validators=[''])
+            m2m = models.ManyToManyField(
+                Model,
+                null=True,
+                validators=[''],
+                limit_choices_to={'name': 'test_name'},
+                through='ThroughModel',
+                through_fields=('modelm2m', 'model'),
+            )
+
+        class ThroughModel(models.Model):
+            model = models.ForeignKey('Model', models.CASCADE)
+            modelm2m = models.ForeignKey('ModelM2M', models.CASCADE)
 
         errors = ModelM2M.check()
         field = ModelM2M._meta.get_field('m2m')
@@ -191,15 +202,19 @@ class RelativeFieldTests(SimpleTestCase):
                 'null has no effect on ManyToManyField.',
                 obj=field,
                 id='fields.W340',
-            )
-        ]
-        expected.append(
+            ),
             DjangoWarning(
                 'ManyToManyField does not support validators.',
                 obj=field,
                 id='fields.W341',
-            )
-        )
+            ),
+            DjangoWarning(
+                'limit_choices_to has no effect on ManyToManyField '
+                'with a through model.',
+                obj=field,
+                id='fields.W343',
+            ),
+        ]
 
         self.assertEqual(errors, expected)