Preheat the oven to 350°F (175°C). Line standard muffin pans with 18 cupcake liners.
Add the softened cream cheese and granulated sugar to a large mixing bowl. Beat until smooth, light, and creamy.
Add the sour cream, pumpkin purée, pumpkin pie spice, and flour. Mix until the pumpkin cheesecake filling is smooth and evenly combined.
Add the eggs and vanilla extract. Mix on low speed just until incorporated. Avoid overmixing once the eggs have been added.
Carefully separate 18 Oreo cookies into halves. Place one cookie half, frosting side facing upward, into the bottom of each cupcake liner.
Divide the cheesecake batter evenly among the 18 liners.
Place another Oreo half on top of each Mini Pumpkin Oreo Cheesecake, frosting side facing down, gently pressing it into the batter.
Bake for approximately 24 minutes, or until the edges appear set and the centers still have a slight jiggle.
Remove the pans from the oven and allow the cheesecakes to cool in the pans for 10–15 minutes.
Carefully transfer them to a wire rack and let them finish cooling.
Refrigerate for at least 2–3 hours, or until completely chilled and firm. For an even better texture, chill overnight.
Crush the remaining two Oreo cookies into crumbs.
Before serving, top each chilled cheesecake with Cool Whip and sprinkle with crushed Oreo crumbs.