Cut butternut squash into 6 rectangles and make even-layered slits, making sure to not cut all the way through.
Place squash, chestnuts and pearl onions on parchment lined baking sheet with melted butter and thyme and roast in preheated oven for 15 minutes. Remove chestnuts and onions after 5 minutes.
Brush butternut squash with molasses and sprinkle with fresh thyme.