Aimed at the maintenance of formation when the leading unmanned aerial vehicle (UAV) maneuvers in three dimensional space in the progress of formation flight, an UAV threedimensional formation maintaining control system is established. According to the UAV formation flight geometry relationship in three dimensional space, the UAV autopilot model and the kinematic model of formation are used to build a threedimensional mathematical model of formation flight in rotating coordinate system. In consideration of the closed loop system with timevarying external disturbance,an adaptive formation keeping controller is designed. Stability of the proposed adaptive control law is analyzed based on Lyapunov theory. Finally, the simulation result demonstrates the controller can suppress the influence of the disturbance effectively and make followers track the leader rapidly and maintain formation stability.