Preheat the oven to 350 degrees F. Line the bottom of a 9-by-9-inch square pan with parchment paper and spray with cooking spray.
In a medium bowl, combine the crumbs, granulated sugar and melted butter and press into the bottom of the prepared pan. Bake until browned, 8 to 10 minutes. Set aside.
Increase the oven temperature to 450 degrees F and make the filling.
Using an electric mixer, beat the cream cheese until fluffy, then add the brown sugar and flour. Add the eggs 1 at a time, beating well after each addition. Add the vanilla. Fold in the chopped pecans.
Pour the batter into the crust and bake for 10 minutes. Reduce the oven temperature to 250 degrees F and bake until slightly browned on top, an additional 50 minutes. Allow to cool completely, about 20 minutes, then refrigerate for at least 2 hours. Cut into 9 bars before serving.