Heat the oven to 325°F. Grease a 9-inch springform pan and wrap the outside with foil if using a water bath.
Mix graham cracker crumbs, sugar, and melted butter. Press into the pan and bake for 8 minutes.
Beat softened cream cheese until smooth. Add sugars, sour cream, vanilla, cinnamon, and nutmeg.
Add eggs one at a time, mixing on low speed only until combined.
Pour over the crust and bake for 55 to 65 minutes, until the edges are set and the center gently wobbles.
Turn off the oven and cool the cheesecake inside for 30 minutes. Chill for at least 6 hours.
Melt butter in a saucepan. Stir in brown sugar, cream, vanilla, and salt. Simmer for 2 to 3 minutes.
Stir in the pecans, cool until warm, and spoon the topping over the chilled cheesecake.