Preheat your oven to 375°F (190°C) and line a muffin tin with muffin liners.
In a large mixing bowl, combine the flour, granulated sugar, brown sugar, baking soda, salt, and pumpkin pie spice.
In another bowl, mix the pumpkin puree, vegetable oil, eggs, milk, and vanilla extract until well combined.
Gradually add the wet ingredients to the dry ingredients, stirring until just combined. Do not overmix.
In a separate bowl, prepare the cream cheese filling by beating the softened cream cheese, granulated sugar, egg yolk, and vanilla extract until smooth and creamy.
Fill each muffin liner halfway with the pumpkin batter.
Add a tablespoon of the cream cheese filling on top of the batter in each muffin liner.
Top with the remaining pumpkin batter, filling each liner about 3/4 full.
Use a toothpick to gently swirl the batter and cream cheese filling together for a marbled effect.
Bake in the preheated oven for 18-20 minutes or until a toothpick inserted into the center of a muffin comes out clean.
Allow the muffins to cool in the tin for 5 minutes before transferring them to a wire rack to cool completely.