Preheat oven to 400°F. With a fork, pierce squash halves several times. Rub the inside of the halves with 1 tablespoon olive oil. Sprinkle with salt and pepper.
On a foil-lined, rimmed baking sheet, arrange squash, flesh side down. Bake 45 to 50 minutes or until very tender. Cool slightly. Shred insides with a fork; set aside.
Meanwhile, in a 12-inch skillet heat remaining 1 tablespoon oil over medium heat. Cook and stir sausage, red pepper, and onion 6 to 8 minutes or until sausage is browned and pepper and onion are crisp-tender.
Add spaghetti squash to skillet and cook and stir until heated through.
Just before serving, carefully stir in pesto, and sprinkle with Parmesan cheese.