Considering drastic vibration phenomena occurred in middle-low speed maglev test line with guide way step, a new control strategy for restraining the disturbance of guide way step effectively is presented. A dynamical two-point levitation model for single electromagnet module running on guide way step is built, and fluctuation of sensor gap and equivalent gap when running on guide way step is analyzed. By adopting state feedback control algorithm, sensor gap and equivalent gap are selected as feedback control variable respectively. Dynamical simulation results show that two control strategies can reflect the fluctuation of sensor gap and equivalent gap, and the control strategy with equivalent gap restrain the disturbance of guide way step effectively.