The concept of Holon is introduced into the intelligent control system of formation navigation so as to improve the autonomous and intelligent level of the vehicles in the process of formation flight. The Holon-based intelligent control architecture of formation navigation is established. The Holon unit model, including communication and cooperation layer, assessment and decision-making layer, coordinating action layer and action execution layer, is presented. The Holon function is analyzed. In the end, the critical technologies for intelligent control system of navigation formation are also proposed.