The low-speed maglev train presented by national maglev transportation engineering R&D center was regarded as the research object. The design of magnetic suspension control (MSC) system under disturbance, nonlinear and time variant was discussed. Firstly, the nonlinear dynamic model of the MSC system was derived and the simulation platform of the MSC system was established. Next, the linear PD control law was designed. The simulation results show its performance depended on parameters and its robust was weak. An improved sliding mode controller was developed to improve the robustness by utilizing exponential reaching law and variable boundary layer. The Lyapunov method was employed to prove its stability. The sufficient simulations show that the presented control method had good dynamic performance, high control accuracy and strong robustness without chattering. Finally, the experiment verified the effectiveness of the improved sliding mode controller.