To reduce the influence of deflection and time lag of control force during the dispersion of tether on trajectory control precision, this paper designed stratospheric satellite control system. According to the system composition this paper established the trajectory control system and the longitude motion model of balloon system; Based on sliding mode variable structure control, according to deflection between the actual instruct position and instruct position in north-south direction, the methods of exponent reaching law and the flutter reduction around boundary layers are used to design the control system of trajectory controller. The simulation results have shown that the control system can overcome the disturbance and time lag caused by tether effectively, and complete the stratosphere satellite east and west direction motion control with the error of 80 m.