Preheat your oven to 325°F (163°C). Line a 9-inch springform pan with parchment paper on the bottom and grease the sides. In a small bowl, combine the graham cracker crumbs, 3 tablespoons packed dark brown sugar, and 10 tablespoons melted unsalted butter. Mix until the crumbs are all evenly moistened. Press the mixture into the bottom and up the sides of the springform pan. Bake the crust for 10 minutes, then remove from the oven and set aside to cool. Wrap the outside of the pan with aluminum foil to prevent water from entering during the water bath process.

Reduce the oven temperature to 300°F (148°C). In a medium saucepan, combine 3 large eggs, 1 cup dark corn syrup, 3/4 cup packed dark brown sugar, 1 teaspoon vanilla extract, 1/4 cup melted unsalted butter, 1/2 teaspoon salt, and 1 1/2 cups chopped pecans. Bring the mixture to a boil over medium-high heat, stirring constantly. Reduce the heat and simmer, stirring continuously, until thickened (about 5–7 minutes). Be careful not to overcook, as this will make the layer too firm. Pour the mixture into the prepared crust from Step 1 and set aside. I like to let this layer cool for a couple of minutes before adding the cheesecake batter so the layers stay distinct.

In a large mixing bowl, add the room temperature cream cheese, 1 cup packed dark brown sugar, and 3 tablespoons all-purpose flour. Beat together on low speed until the mixture is smooth and combined, scraping down the sides of the bowl as needed. Add 3/4 cup sour cream and 1 1/2 tablespoons vanilla extract, and mix again on low speed until just combined. Next, add the 3 large eggs (room temperature) one at a time, mixing slowly on low speed after each addition and scraping the bowl as needed. This method helps prevent adding too much air, minimizing the risk of cracks. Pour the cheesecake batter over the pecan pie layer from Step 2, drizzling slowly and evenly to avoid displacing the pecan filling.

Place the filled springform pan inside a larger pan and fill the larger pan with warm water until it comes about halfway up the sides of the springform pan, keeping the foil barrier intact. Bake at 300°F (148°C) for 1 hour and 10–15 minutes. The center should be set but still slightly wobbly. Turn off the oven and leave the door closed for 30 minutes to let the cheesecake cook gently as it starts to cool. Next, crack the oven door and let the cheesecake cool for another 30 minutes. This slow cooling helps prevent cracks. Remove from the oven and water bath, then chill in the refrigerator until completely firm (approximately 5–6 hours or overnight). I like to let it chill overnight for the best texture.

Once the cheesecake is cold and set, prepare the topping. In a medium saucepan, combine 1 cup packed dark brown sugar, 1/2 cup heavy whipping cream, 1/2 cup cubed unsalted butter, and 1 tablespoon dark corn syrup (optional). Heat over medium-low heat until the butter and sugar have melted fully. When the sugar has dissolved, increase the heat to medium and bring the mixture to a full boil, stirring constantly for 1–2 minutes. Remove from heat and stir in 1 1/2 cups toasted chopped pecans, 1/2 teaspoon salt, and 1 teaspoon vanilla extract. Allow to cool in the fridge to just above room temperature—the topping should still be spreadable, not fully cold, so it sits nicely on the cheesecake. If it becomes too firm, briefly reheat in the microwave. I like to taste the caramel and add a pinch of salt if I want to cut some of the sweetness.

Remove the fully chilled cheesecake from the springform pan and transfer it to a serving platter. Spread the cooled pecan caramel topping from Step 5 evenly over the top of the cheesecake. Cover and refrigerate until ready to serve. This cheesecake is best enjoyed within 4–5 days. For an extra touch, I like to sprinkle a little ground cinnamon (if using) over the caramel topping for added warmth and flavor.