Mix the graham cracker crumbs and butter in a large bowl until evenly moistened; press into the bottom of a 9-inch springform pan.
Bake in the preheated oven until the crust has lightly browned and smells toasted, about 5 minutes. Remove from the oven and allow to cool.
Beat the cream cheese, sugar, and sour cream with an electric mixer in a large bowl until light and fluffy. Beat in the eggs, one at a time, allowing each egg to blend into the cream cheese mixture before adding the next. Beat the flour, vanilla extract, and lime juice into the cream cheese mixture with the last egg. Fold the jalapeno pepper into the mixture; mixing just enough to evenly combine. Pour into the prepared crust.
Bake in the preheated oven for 15 minutes. Reduce heat to 250 degrees F (120 degrees C) and continue baking until the center has just set, 50 to 55 minutes. Remove from the oven, run the tip of a paring knife around the edges of the pan, set the pan on a wire rack, and allow the cheesecake to cool at room temperature for 1 hour before placing into the refrigerator, and cooling 4 hours to overnight.