To reduce quality and precision of railway, and improve the capacity of anti-jamming of maglev train. Basing on the two-point levitation model of single electromagnet module, the signals of the sensors, such as suspension gap and electromagnet vertical speed, can be used to analyze the differences between the vibrations when running across the railway step and arisen by other disturbance; a new method is put forward for identifying the railway step accurately. According to the step railway information, compensate the scheduled gap. Simulation result shows that the algorithm can restrain the disturbance of railway step effectively.