In a large stock pot, heat coconut oil over medium-high heat. Add onion and cook until softened, about 3 minutes. Add garlic, ginger, and red curry paste and stir until fragrant, about 30 seconds. Add butternut squash, sweet potato, and vegetable broth. Bring to a boil, cover, and lower to a simmer. Simmer until squash and sweet potato are fork tender, 10-15 minutes.
Use an immersion blender (or blend in small batches in a regular blender) to blend until smooth. Stir in coconut sugar, salt and pepper, fresh lime juice, and coconut milk.
Top with cilantro and crushed red pepper flakes before serving.