Bring a large pot of salted water to a boil. Add the spaghetti and cook according to package instructions until al dente, about 9 to 11 minutes. Drain and set aside.
While the pasta cooks, heat olive oil in a large skillet over medium heat.
Add the chopped onion and sauté for 4 to 5 minutes until softened and translucent.
Add the minced garlic and cook for 1 minute until fragrant.
Add the ground beef to the skillet. Cook, breaking it up with a spoon, until browned and no longer pink, about 6 to 8 minutes. Drain excess fat if necessary.
Stir in the crushed tomatoes, tomato paste, dried oregano, dried basil, salt, black pepper, and red pepper flakes.
Reduce heat to low and simmer the sauce for 15 minutes, stirring occasionally.
Add the cooked spaghetti to the skillet with the meat sauce and toss to combine evenly.
Remove from heat and stir in the grated Parmesan cheese and chopped fresh parsley.
Divide the pasta among plates and serve with extra Parmesan cheese on the side.