Preheat your oven to 325°F (160°C). In a mixing bowl, combine the graham cracker crumbs, melted butter, and granulated sugar. Mix until the crumbs are evenly moistened. Press this mixture firmly into the bottom of a 9-inch springform pan to create an even layer. Bake in the oven for 10 minutes to set, then remove and let cool completely.
In a large mixing bowl, beat the softened cream cheese and 1 cup of granulated sugar together with an electric mixer on medium speed until the mixture is smooth and creamy with no lumps. Add the sour cream and mix until well combined. Add the eggs one by one, mixing on low speed just until incorporated after each addition. Finally, stir in the pure vanilla extract to flavor the cheesecake filling.
In a separate medium bowl, toss the thinly sliced apples with ground cinnamon and ground nutmeg until the apple slices are fully coated in the spice mixture.
Pour half of the cheesecake batter over the cooled graham cracker crust in the springform pan. Evenly layer half of the spiced apple slices on top of the batter and drizzle with half of the salted caramel sauce. Carefully pour the remaining cheesecake batter on top, smoothing it out gently. Arrange the rest of the apple slices over the second layer of batter and drizzle with the remaining salted caramel sauce.
Place the assembled cheesecake into the preheated oven and bake for 50-60 minutes. The center of the cheesecake should be set but may still have a slight jiggle to it. Once done, turn off the oven and leave the cheesecake inside with the door slightly ajar for one hour to cool gradually, helping to prevent any cracks from forming.
After the one-hour cooling period, transfer the cheesecake to the refrigerator and chill for at least 4 hours, but preferably overnight for the best texture and flavor.
When ready to serve, gently run a knife around the edge of the springform pan before removing the sides. Drizzle additional salted caramel sauce over the top and finish with a sprinkle of flaky sea salt for a beautiful presentation contrast.