Preheat the oven to 325°F.
In a medium-sized bowl mix together the graham cracker crumbs, finely chopped pecans, sugar, and melted butter until fully combined.
Press this mixture into a 9-inch springform pan on the bottom and up the sides. I like to use the bottom of a flat measuring cup to pack it in. Place in the refrigerator until ready to use.
In the bowl of a stand mixer or in a large bowl with an electric hand mixer, whip the cream cheese until smooth with no lumps. Slowly add in the sugar until combined.
Add the eggs one at a time until fully incorporated, making sure the first one is mixed in before adding the next.
Mix in the sour cream, vanilla, cinnamon, and nutmeg until smooth.
Wrap your springform pan that has the crust in it well with heavy-duty foil. Pour the cheesecake mixture into the crust.
Place the cheesecake into a large roasting pan. Fill the pan halfway up the side of the cheesecake pan with hot water.
Reduce the oven temperature to 300°F. Bake for 1 hour and 30 minutes, turn off the heat, and let the cheesecake sit in the oven for an additional hour, until the center is set. It will still be slightly jiggly.
Remove the cheesecake from the oven and place it on the counter. Let it cool to room temperature, then place in the refrigerator for at least 8 hours, up to overnight.
Just before serving, make the pecan pie topping. In a small saucepan place the butter, heavy cream, sugar, brown sugar, corn syrup, baking soda, cinnamon, salt, and nutmeg.
Place over medium heat, stirring constantly until everything is melted.
Bring to a boil, reduce heat to low, and simmer, stirring occasionally for 8 minutes. The mixture will darken and thicken.
After 8 minutes take off the heat, add the pecans and vanilla, stir them in to combine. Let the mixture cool for 10 minutes.
Take your cheesecake out of the springform pan and place it on your serving platter. Spoon the pecan mixture evenly on top. Serve immediately.