Preheat the oven to 425 degrees and line a baking sheet with parchment paper. Set aside.
Prepare the squash for baking by brushing the inside with 1 Tablespoon of the olive oil and sprinkling with salt and pepper to taste. Turn the squash face down (skin up) and bake for about 45 minutes or until tender and cooked through.
Meanwhile, in a large pot heat the remaining 2 Tablespoons of oil and cook the onion over medium heat until transparent and tender. Add garlic and cook 1 additional minute. Set aside.
When the squash is done, scoop out the inside and discard the skin. Place the squash, cooked onions and garlic, vegetable broth, salt, pepper, cinnamon, thyme and honey in a blender. Blend on medium high speed until pureed and smooth. You may need to work in batches, depending on the size of your blender.
Return the soup into the large pot and place on medium low until heated through.