Aiming at the formation keeping problem of Unmanned Aerial Vehicles (UAVs) in three-dimensional space formation flight after implementation of rendezvousing, a three-dimensional formation keeping system based on a virtual leader is proposed. Based on the three-dimensional kinematics relationship of UAV flight, and combined with the simplified UAV autopilot model, a relative kinematic model is established based on the rotating coordinate system with the virtual leader as reference. The UAV formation keeping controller is designed by the sliding mode variable structure control method. The simulation verification shows that, the controller can enable the UAVs to track the maneuvering virtual leader and maintain the formation stability, and the response accuracy and speed are ideal.