Preheat oven to 425°F (218°C). Spray a 12-count muffin pan with nonstick spray or line with cupcake liners.

Mix the brown sugar, cinnamon, and melted butter together in a small bowl until combined. Add the flour and use a fork to gently mix until crumbs form. Set aside.

Whisk the flour, baking powder, baking soda, salt, cinnamon and pumpkin pie spice together in a large bowl. Set aside.

In a medium bowl, whisk the brown sugar, granulated sugar, eggs, pumpkin, oil, milk, and vanilla extract together. Pour the wet ingredients into the dry ingredients and whisk or stir until just combined.

Using a handheld or stand mixer fitted with a paddle or whisk attachment, beat the cream cheese in a medium bowl on medium-high speed until smooth and creamy. Beat in the egg yolk, vanilla extract, and sugar until combined.

Spoon 1 heaping Tablespoon of pumpkin muffin batter into the muffin cups. Layer with about 1 spoonful of cheesecake filling, then another heaping Tablespoon of muffin batter.

Sprinkle crumb topping onto each, then press it down into the tops of the muffins.

Bake for 5 minutes at 425°F (218°C), then reduce heat to 350°F (177°C) and continue baking for another 15-17 minutes.

Allow to cool for at least 10 minutes in the pan before serving.