class Model1(models.Model):
    name = models.CharField()
    ....
class Model2(models.Model):
    model1 = models.ForeignKey(Model1)
    name = models.CharField()
    model3 = models.ForeignKey(Model3)
    ...
class Model3(models.Model):
    name = models.CharField()
    ...

LIST = [2,23,54]

pk_list = None
for value in LIST:
    if pk_list:
        pk_list = Model2.objects.filter(
            model3__pk=value,
            model1_id__in=pk_list).values_list(
                'model1_id', flat=True)
    else:
        pk_list = Model2.objects.filter(
            model3__pk=value).values_list(
                'model1_id', flat=True)

Model1.objects.filter(model2__model3__pk__in=LIST)