Preheat oven to 425 degrees and line a baking sheet with foil or parchment. Halve the squashes, then scoop out the innards.
Melt butter and add in the maple syrup and sea salt. Stir. Brush the cut sides of the squash with the mixture, letting it form a puddle in the middle of each squash half.
Add the walnuts to the remaining syrup mixture and set aside.
Bake the squash 1 hour. Remove from the oven and scoop the walnut mixture evenly into each squash. Return squash to the oven and bake for 10-12 more minutes, until the flesh is just beginning to brown.
Remove from oven and garnish with pumpkin seeds and fresh thyme leaves. Add salt and pepper to taste.