Preheat your oven to 350°F (175°C). Line a muffin pan with cupcake liners or grease with cooking spray.
In a medium bowl, combine graham cracker crumbs and sugar. Pour in the melted butter and mix until well combined.
Press about one tablespoon of the crumb mixture into the bottom of each muffin liner, creating a compact layer. Bake for 5 minutes, then remove from the oven.
Reduce the oven temperature to 300°F (150°C). Chop the apple pie filling into smaller pieces and mix in the cinnamon and caramel sauce. Set aside.
In a large bowl, beat the softened cream cheese using a hand mixer until smooth and fluffy, about 2-3 minutes.
Add the vanilla and sugar to the cream cheese. Beat until combined, then add eggs, one at a time, mixing until just blended.
Spoon a layer of the apple filling mixture over the pre-baked crusts in each muffin liner.
Fill each muffin liner about 3/4 full with the cream cheese mixture, covering the apple layer.
Bake in the preheated oven for 20-25 minutes until the edges are set and the center is slightly jiggly.
Remove from the oven and allow to cool to room temperature before transferring to the refrigerator. Chill for at least 3 hours before serving.