Roll out the pizza dough and shape into a round circle to fit a 10 inch pizza pan. Slide the dough onto the pan.
Stir the squash and cranberry sauce together in a bowl until smooth. Spoon the squash mixture over the pizza dough so it's even but not too thick. Sprinkle the sauce with the Cheddar and Parmesan cheeses. Sprinkle the pecans over the cheese.
Bake in preheated oven until cheese is melted. Remove pizza from the oven, slide onto a serving plate, and cut into wedges. Serve immediately.