Preheat the oven to 375 degrees F (190 degrees C). Spray a 9x13-inch baking dish with cooking spray.

Make crust: Stir together flour, pecans, and melted butter 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. Place in the refrigerator to cool completely.

Make first layer: Stir together cream cheese, whipped topping, and confectioners’ sugar in a bowl until smooth; spread over cooled crust. Set aside.

Make second layer: Whisk together milk and instant pudding 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.

Add third layer: Top pudding layer with whipped topping. Refrigerate until flavors blend and pie is set, about 24 hours.