Heat a large nonstick saucepan coated with cooking spray over medium-high heat. Add onion and garlic; saute 3 minutes or until tender. Add broth and broccoli. Bring broccoli mixture to a boil over medium-high heat. Reduce heat to medium; cook 10 minutes.
Combine milk and flour, stirring with a whisk until well blended. Add milk mixture to broccoli mixture. Cook 5 minutes or until slightly thick, stirring constantly. Stir in pepper. Remove from heat; add cheese, stirring until cheese melts.
Place one-third of the soup in a blender or food processor, and process until smooth. Return pureed soup mixture to pan.