Preheat oven to 400 degrees.
Cut spaghetti squash in half and drizzle 1 tbsp olive oil over squash. Season with salt and pepper.
Place squash on a baking sheet and bake in the oven for 30-40 minutes or until squash is soft enough to remove the insides with a fork.
While squash is cooking, wash and shred carrots and zucchini.
When squash is done cooking, remove from oven and let cool.
While squash is cooling, heat 1 tbsp olive oil in a pan over medium heat. Add garlic and cook for 1-2 minutes.
Add crushed tomatoes, tomato puree, thyme, salt, pepper and red pepper flakes to pan.
Allow mixture in pan to simmer on stove to let flavors blend.
Once squash has cooled, take a fork and scrape out the inside and place it into the tomato mixture.
Add in shredded carrots and zucchini and cook for 5-10 minutes.
Remove from stove and top with shredded parmesan cheese.