Line an 8x8 inch baking pan with parchment paper (can use a 7x11 inch pan as well), or spray with cooking spray. Preheat oven to 350 F degrees.
Mix brownies according to package directions and pour into prepared pan, smoothing into an even layer, reserving 1/2 cup for later.
In a small mixing bowl, combine cream cheese, pumpkin, both sugars, egg and pumpkin pie spice. Pour over brownie batter and smooth into an even layer.
Drop the reserved brownie batter by the spoonful over the cheesecake layer, then gently swirl the two layers together with a toothpick or butter knife. Be sure not to mix, you're just looking for swirls.
Combine the pecans, brown sugar, flour, melted butter and pumpkin pie spice in a small bowl, then sprinkle over the top of the brownies.
Bake for 55 minutes, until brownies are set and the edges are starting to brown. If the middle is a tad bit soft, it will firm up as it cools.