Preheat oven to 350°F. Grease a 9-inch springform pan.
In a medium bowl, combine graham cracker crumbs, brown sugar, cinnamon, and melted butter. Press into the bottom of the pan. Bake for 8 minutes. Let cool.
In a large bowl, beat cream cheese, sugar, and vanilla until smooth. Add eggs one at a time, mixing after each addition.
Stir in mashed sweet potatoes, cinnamon, nutmeg, and mix well.
Pour the batter into the cooled crust and smooth the top. Bake for 50–60 minutes or until the center is set. Let cool to room temperature.
In a bowl, combine brown sugar, flour, melted butter, and chopped pecans. Spread evenly over the top of the cooled cheesecake.
Refrigerate the cheesecake for at least 4 hours or overnight before serving.