diff --git a/django/db/models/sql/query.py b/django/db/models/sql/query.py
index f8e146b8dee..375e22c4de1 100644
--- a/django/db/models/sql/query.py
+++ b/django/db/models/sql/query.py
@@ -390,7 +390,7 @@ class Query(BaseExpression):
             else:
                 # Reuse aliases of expressions already selected in subquery.
                 for col_alias, selected_annotation in self.annotation_select.items():
-                    if selected_annotation == expr:
+                    if selected_annotation is expr:
                         new_expr = Ref(col_alias, expr)
                         break
                 else:
diff --git a/docs/releases/3.0.7.txt b/docs/releases/3.0.7.txt
index 5457e59b3d9..0f1188724a8 100644
--- a/docs/releases/3.0.7.txt
+++ b/docs/releases/3.0.7.txt
@@ -15,3 +15,6 @@ Bugfixes
 * Fixed a regression in Django 3.0 where ``QuerySet.values()`` and
   ``values_list()`` crashed if a queryset contained an aggregation and a
   subquery annotation (:ticket:`31566`).
+
+* Fixed a regression in Django 3.0 where aggregates used wrong annotations when
+  a queryset has multiple subqueries annotations (:ticket:`31568`).
diff --git a/tests/aggregation/test_filter_argument.py b/tests/aggregation/test_filter_argument.py
index 0c8829efdf6..650cb8e4606 100644
--- a/tests/aggregation/test_filter_argument.py
+++ b/tests/aggregation/test_filter_argument.py
@@ -2,7 +2,8 @@ import datetime
 from decimal import Decimal
 
 from django.db.models import (
-    Avg, Case, Count, F, OuterRef, Q, StdDev, Subquery, Sum, Variance, When,
+    Avg, Case, Count, Exists, F, Max, OuterRef, Q, StdDev, Subquery, Sum,
+    Variance, When,
 )
 from django.test import TestCase
 from django.test.utils import Approximate
@@ -120,3 +121,23 @@ class FilteredAggregateTests(TestCase):
             cnt=Count('pk', filter=Q(earliest_book_year=2008)),
         )
         self.assertEqual(aggs['cnt'], 2)
+
+    def test_filtered_aggregate_ref_multiple_subquery_annotation(self):
+        aggregate = Book.objects.values('publisher').annotate(
+            has_authors=Exists(
+                Book.authors.through.objects.filter(book=OuterRef('pk')),
+            ),
+            authors_have_other_books=Exists(
+                Book.objects.filter(
+                    authors__in=Author.objects.filter(
+                        book_contact_set=OuterRef(OuterRef('pk')),
+                    )
+                ).exclude(pk=OuterRef('pk')),
+            ),
+        ).aggregate(
+            max_rating=Max(
+                'rating',
+                filter=Q(has_authors=True, authors_have_other_books=False),
+            )
+        )
+        self.assertEqual(aggregate, {'max_rating': 4.5})