In a large bowl, whisk lemon pudding mix with 2 cups cold milk until mixture thickens significantly (about 1-2 minutes). Let chill briefly.
In another bowl, combine softened cream cheese, powdered sugar, and 1 teaspoon vanilla extract until smooth.
Toss fresh blueberries with 2 tablespoons lemon juice to make a tart compote.
Crush graham crackers into coarse crumbs using a food processor or by hand.
Layer chilled pudding, cream cheese mixture, blueberry compote, and graham cracker crumbs in a parfait glass or jar. Repeat layers as desired.
Chill for 30 minutes before serving.