Preheat oven to 425°F.
Toss squash, onion, apple, ¼ cup oil, 2 tablespoons thyme, ½ teaspoon plus ⅛ teaspoon salt and ¼ teaspoon pepper together on a large rimmed baking sheet; spread in a single layer.
Roast, stirring once, until the squash and onion are tender and golden brown, 35 to 40 minutes.
Transfer the squash mixture and any drippings from the pan to a blender; add 3 cups broth and 1 cup cream.
Secure lid on blender; remove center piece to allow steam to escape. Place a clean towel over the opening.
Process until smooth, about 1 minute.
Garnish with additional thyme and pepper, if desired.
