Prepare the Baking Pan: Preheat the oven to 325°F (163°C). Line an 8-inch square baking pan with parchment paper, leaving some overhang on two sides. Lightly grease any exposed sides if needed.
Make the Graham Cracker Crust: Combine the graham cracker crumbs, melted butter, and sugar in a mixing bowl. Stir until the crumbs resemble damp sand. Press firmly into the prepared pan and bake for 8–10 minutes. Let the crust cool slightly.
Prepare the Cheesecake Filling: Beat the softened cream cheese and sugar until smooth and creamy. Add the eggs one at a time, mixing on low speed. Stir in the vanilla extract and sour cream until combined, scraping down the sides of the bowl as needed.
Mix the Pumpkin Filling: Transfer approximately one-third of the cheesecake mixture to a separate bowl. Stir in the pumpkin puree, pumpkin pie spice, cinnamon, and flour until smooth and evenly combined.
Layer and Swirl the Fillings: Spread the remaining plain cheesecake mixture over the crust. Spoon the pumpkin mixture over the top in small dollops. Gently swirl with a butter knife to create a marbled pattern.
Bake Until Set: Bake at 325°F (163°C) for approximately 35–45 minutes, until the edges are set and the center has a slight wobble. Avoid overbaking. Cool at room temperature, then refrigerate within two hours.
Chill, Slice, and Serve: Refrigerate for at least 4 hours or until completely firm. Lift the cheesecake from the pan using the parchment paper and cut into squares with a sharp knife, wiping the blade between cuts. Serve chilled with optional whipped cream and cinnamon.