Preheat your oven to 375°F (190°C). Grease a 9×13-inch baking dish and set aside.
Cook the mostaccioli pasta according to the package instructions until al dente. Drain and set aside.
In a large skillet, cook the Italian sausage over medium heat, breaking it apart with a spoon, until browned and cooked through, about 5-7 minutes. Remove any excess grease from the skillet.
Add the chopped onion to the skillet with the sausage and cook until softened, about 5 minutes. Add the minced garlic and cook for an additional 1-2 minutes until fragrant.
Stir in the crushed tomatoes, diced tomatoes, dried oregano, dried basil, dried thyme, salt, and pepper. Simmer the sauce for about 10 minutes, stirring occasionally.
Add the cooked mostaccioli pasta to the skillet with the sauce and toss to combine until the pasta is evenly coated.
Transfer the pasta mixture to the prepared baking dish. Sprinkle the shredded mozzarella cheese and grated Parmesan cheese evenly over the top.
Cover the baking dish with aluminum foil and bake in the preheated oven for 20 minutes. Then, remove the foil and bake for an additional 10-15 minutes, or until the cheese is melted and bubbly.
