Preheat oven to 375 degrees F. Spray muffin tin with non-stick spray or fill with liners.
In a medium mixing bowl, whisk together the flour, cinnamon, baking soda, and salt.
In a large mixing bowl, mix pumpkin puree, sugar, and brown sugar. Beat egg with a fork then add the egg, oil, and vanilla to the pumpkin mixture.
Slowly whisk the flour mixture into the pumpkin mixture. Mix until there are no lumps.
Fill muffin tins ¾ full.
In a medium bowl, beat cream cheese until smooth. You can mix by hand or with an electric mixer.
Add in sugar, egg yolk, and salt. Mix until well combined.
Top each muffin with 1 tablespoon of the cream cheese mixture. Use a toothpick or fork to swirl it into the batter creating a marbling effect.
Bake the muffins for 18-22 minutes, or until a toothpick inserted in the center comes out clean. I baked mine for 22 minutes, but it depends on how large your muffins are.
Store any leftovers in an airtight container in the refrigerator. They'll be good for 3 days in the fridge.