Heat the oven to 325°F (165°C). Line a 9x13-inch baking pan with parchment paper, leaving about 2 inches of overhang on the two long sides so you can lift the bars out later.
Stir the graham cracker crumbs, granulated sugar, cinnamon, salt, and melted butter in a medium bowl until the mixture looks like damp sand. Press firmly and evenly into the bottom of the pan with the bottom of a measuring cup. Bake for 10 minutes, then set aside to cool slightly. Leave the oven on.
Beat the softened cream cheese and granulated sugar in a large bowl on medium speed until completely smooth and creamy, about 2 minutes, scraping down the bowl halfway through.
Add the eggs one at a time, beating on low just until each disappears. Beat in the sour cream and vanilla until smooth.
Scoop out 1 1/2 cups of the plain cheesecake batter into a separate bowl and set it aside — this becomes the vanilla swirl.
To the remaining batter, add the pumpkin puree, brown sugar, pumpkin pie spice, cinnamon, nutmeg, salt, and flour. Beat on low just until smooth and evenly orange. Do not overbeat — extra air causes cracks.
Pour the pumpkin batter over the baked crust and smooth the top with an offset spatula.
Drop large spoonfuls of the reserved vanilla batter over the pumpkin layer, then drag a butter knife through the dollops in long S-curves to marble the top. Do not over-swirl or the layers will blend into one color.
Bake at 325°F (165°C) for 40–45 minutes, until the edges are set and lightly puffed and the center still has a slight jiggle like set gelatin when you gently shake the pan.
Cool in the pan on a wire rack for 1 hour, then cover and refrigerate for at least 4 hours, preferably overnight, before slicing.
Lift the slab out by the parchment overhang. Cut into 24 bars with a long, sharp knife, wiping the blade clean with a hot, damp cloth between cuts. Serve chilled or at cool room temperature, with whipped cream and a dusting of cinnamon if you like.