diff --git a/django/db/models/base.py b/django/db/models/base.py
index 9cc1af0171..11a2d2a264 100644
--- a/django/db/models/base.py
+++ b/django/db/models/base.py
@@ -1301,12 +1301,13 @@ class Model(metaclass=ModelBase):
         fields = (f for f in fields if isinstance(f.remote_field.through, ModelBase))
 
         for f in fields:
-            signature = (f.remote_field.model, cls, f.remote_field.through)
+            signature = (f.remote_field.model, cls, f.remote_field.through, f.remote_field.through_fields)
             if signature in seen_intermediary_signatures:
                 errors.append(
                     checks.Error(
-                        "The model has two many-to-many relations through "
-                        "the intermediate model '%s'." % f.remote_field.through._meta.label,
+                        "The model has two identical many-to-many relations "
+                        "through the intermediate model '%s'." %
+                        f.remote_field.through._meta.label,
                         obj=cls,
                         id='models.E003',
                     )
diff --git a/docs/ref/checks.txt b/docs/ref/checks.txt
index a84d9b60b6..42296f65c9 100644
--- a/docs/ref/checks.txt
+++ b/docs/ref/checks.txt
@@ -252,8 +252,8 @@ Models
 * **models.E001**: ``<swappable>`` is not of the form ``app_label.app_name``.
 * **models.E002**: ``<SETTING>`` references ``<model>``, which has not been
   installed, or is abstract.
-* **models.E003**: The model has two many-to-many relations through the
-  intermediate model ``<app_label>.<model>``.
+* **models.E003**: The model has two identical many-to-many relations through
+  the intermediate model ``<app_label>.<model>``.
 * **models.E004**: ``id`` can only be used as a field name if the field also
   sets ``primary_key=True``.
 * **models.E005**: The field ``<field name>`` from parent model ``<model>``
diff --git a/tests/invalid_models_tests/test_models.py b/tests/invalid_models_tests/test_models.py
index 9dd2fd1f06..709d73d6c8 100644
--- a/tests/invalid_models_tests/test_models.py
+++ b/tests/invalid_models_tests/test_models.py
@@ -771,13 +771,35 @@ class OtherModelTests(SimpleTestCase):
 
         self.assertEqual(Group.check(), [
             Error(
-                "The model has two many-to-many relations through "
+                "The model has two identical many-to-many relations through "
                 "the intermediate model 'invalid_models_tests.Membership'.",
                 obj=Group,
                 id='models.E003',
             )
         ])
 
+    def test_two_m2m_through_same_model_with_different_through_fields(self):
+        class Country(models.Model):
+            pass
+
+        class ShippingMethod(models.Model):
+            to_countries = models.ManyToManyField(
+                Country, through='ShippingMethodPrice',
+                through_fields=('method', 'to_country'),
+            )
+            from_countries = models.ManyToManyField(
+                Country, through='ShippingMethodPrice',
+                through_fields=('method', 'from_country'),
+                related_name='+',
+            )
+
+        class ShippingMethodPrice(models.Model):
+            method = models.ForeignKey(ShippingMethod, models.CASCADE)
+            to_country = models.ForeignKey(Country, models.CASCADE)
+            from_country = models.ForeignKey(Country, models.CASCADE)
+
+        self.assertEqual(ShippingMethod.check(), [])
+
     def test_missing_parent_link(self):
         msg = 'Add parent_link=True to invalid_models_tests.ParkingLot.parent.'
         with self.assertRaisesMessage(ImproperlyConfigured, msg):