Toss the squash, onion, olive oil, 1/2 cup Italian bread crumbs, thyme, and blue cheese in a large mixing bowl. Season with salt and pepper. Pour the mixture into a large baking dish. Sprinkle 1/4 cup bread crumbs over the squash.
Bake in the preheated oven until lightly browned on top, 35 to 40 minutes.