Preheat oven to 350 degrees F. Coat an 8×8-inch square baking dish with cooking spray and set aside.
In a food processor, combine graham cracker pieces, sugar, brown sugar and salt. Pulse until fine crumbs form. Add melted butter and pulse until crumbs are moistened. Press crumbs into the bottom of prepared baking dish and bake in the preheated oven for 10 minutes.
In a large bowl, combine cream cheese, milk, eggs, sugar and flour. Using a hand-held mixer on medium speed, mix until smooth. Add lemon zest and juice and mix until combined. Add blueberries (minus a handful) and gently fold in with a spoon.
Pour the cream cheese-blueberry mixture over the crust. Drop the reserved handful of blueberries over the top and bake in preheated oven for 45 minutes. Let cool completely and refrigerate for a minimum of 4 hours before serving.