Preheat your oven to 400 degrees F.
Cut the acorn squash in half lengthwise and scoop out the seeds and stringy pulp.
Brush the cut sides of the squash with 3 tablespoons of olive oil and season generously with salt and pepper.
Place the squash cut-side down on a baking sheet and roast for 30-35 minutes until tender.
While the squash roasts, heat the remaining 3 tablespoons of olive oil in a large skillet over medium-high heat.
Add the chicken sausage and cook until browned, breaking it up into small pieces with a spoon.
Stir in the diced onion and celery, sautéing until softened, about 5 minutes.
Add the garlic, apples, sage, and thyme; cook for an additional 3-4 minutes until the apples are tender.
Stir in the panko breadcrumbs and red pepper flakes, then remove from heat.
Once the squash is tender, flip the halves over and fill the cavities generously with the sausage and apple mixture.
Sprinkle the tops with the grated parmesan cheese.
Return the squash to the oven and bake for another 10-15 minutes, or until the filling is golden and heated through.