Preheat oven to 325°F (163°C). Line a muffin tin with cupcake liners.
In a bowl, mix graham cracker crumbs, sugar, cinnamon, and melted butter. Press about a tablespoon into each liner and bake for 5 minutes.
In a separate bowl, beat cream cheese, sugar, and vanilla until smooth. Add eggs one at a time, mixing well after each.
Remove 1/3 cup of batter and mix it with pumpkin puree, cinnamon, nutmeg, and ginger.
Divide the plain cheesecake batter evenly over the crusts. Spoon the pumpkin batter on top and swirl using a toothpick.
Bake for 20-22 minutes or until set. Let cool and refrigerate for at least 2 hours before serving.