Prepare your baking pan and oven. Preheat your oven to 325°F (165°C). Line a 9×9-inch baking pan with parchment paper, leaving some overhang on the sides for easy removal later.
Make the graham cracker crust. In a medium bowl, combine graham cracker crumbs, sugar, and cinnamon. Pour in melted butter and mix until the mixture resembles wet sand. Press firmly and evenly into the bottom of your prepared pan.
Pre-bake the crust for 10 minutes, then remove from oven and set aside to cool slightly while preparing the filling. Keep the oven on.
Prepare the cheesecake base. In a large bowl, beat the softened cream cheese and sugar with an electric mixer until completely smooth and fluffy, about 2-3 minutes. Add eggs one at a time, beating well after each addition. Mix in vanilla extract.
Divide the cheesecake mixture. Set aside about 1 cup of the plain cheesecake mixture in a separate bowl.
Create the pumpkin layer. To the remaining larger portion of cheesecake mixture, add pumpkin puree, pumpkin pie spice, cinnamon, nutmeg, and flour. Beat until smooth and well combined.
Layer the fillings. Pour the pumpkin cheesecake mixture over the pre-baked crust, spreading it evenly. Carefully drop spoonfuls of the reserved plain cheesecake mixture on top and swirl gently with a knife or toothpick for a marbled effect.
Bake the cheesecake bars for 35-40 minutes, until the edges are set but the center still has a slight jiggle when you gently shake the pan.
Cool completely before cutting. Let cool at room temperature for 1 hour, then refrigerate for at least 3 hours or overnight before cutting into bars.