Preheat oven to 375 degrees F (190 degrees C). Spray a 9x13-inch baking dish with cooking spray.
Stir flour, pecans, and butter together in a bowl; press into the bottom of the prepared baking dish.
Bake in the preheated oven until crust is golden and crisp, about 15 minutes. Cool completely.
Stir cream cheese, 1 cup whipped topping, and confectioners' sugar together in a bowl until smooth; spread over cooled crust.
Whisk milk and pudding together in a bowl until slightly thickened, about 2 minutes. Let sit until pudding is set, about 5 minutes. Spread pudding mixture over cream cheese layer. Top cream cheese layer with 12 ounces whipped topping. Refrigerate until flavors blend and pie is set, about 24 hours.