Preheat the oven to 350 degrees Fahrenheit.
Cut the butternut squash in half lengthwise.
Place squash on a baking dish, cut side up.
Pour ¼ inch of water in the baking dish.
Brush butternut squash flesh with a small amount of olive oil.
Bake in the oven for 90 minutes.
When flesh is tender and easily pierced with a fork, remove the butternut squash and let it cool.
When cool, remove the seeds with a spoon and discard.
Scoop out the flesh and place in a blender. Discard the skin.
Blend until smooth.
Boil pasta according to the directions.
In a large pot, saute onion in olive oil until translucent. Add garlic and cook until fragrant.
Place butternut squash in the large pot and mix to warm.
Add cream cheese and seasonings. Heat on medium heat until cream cheese has melted. (You may add water or milk to thin the sauce if desired.)
Add cooked pasta and toss to coat evenly.
Serve topped with parmesan cheese.