Melt butter in a large pot over medium heat. Sauté onion and apple until they begin to soften, about 5 minutes. Add the squash, carrots, garlic and spices, continue to cook for 5 more minutes.
Add the vegetable stock and bring to a boil. Reduce to a simmer and cook until vegetables are very soft, about 20 minutes.
Remove from heat and cool slightly. Puree with food processor or blender until thick and creamy.
Return soup to stove set over low heat, stir in coconut milk, fresh thyme and cook for another 2-3 minutes. Taste and adjust seasonings as needed. Garnish as desired.