Place whole butternut squash in a pan and place in oven. Bake on 400 for 20 minutes, turn over whole squash and return to oven for additional 15 minutes. Remove from oven and let cool.
Meanwhile peel, core, and slice apples. Place in a saucepan over low heat. Mixthe cinnamon, sugar, and cornstarch in a bowl. Sprinkle over apples and stir, add water and stir. Cover pot and let simmer. Stir occasionally until apples are soft, about 25 minutes.
Slice squash in half vertically and scoop out the seeds from the middle. Extend the hole along the lenght of the squash to allow more room for apple filling.
Lower oven to 350. Fill squash halves with apple mixture. Cover pan tightly with foil and bake fro 40 minutes. Serve warm.