The correct processing of gap signal of levitation sensor is an important basis to realize the stable levitation control of maglev trains. A signal interference will be led to by an improper processing of clearance signal with maglev trains passing through rail cracks, which is liable to cause excessive adjustment of suspension control, affect the stability of suspension system, and even lead to vibration or rail smashing of maglev trains. With a view to solving the problem that maglev trains are prone to vibrate or smash the rail when passing through rail gaps, a new algorithm has been proposed for processing the gap signal of the maglev train passing through rail gaps based on the characteristics of the gap signal data of the maglev train passing through rail gaps of the experimental lines and a certain maglev operation lines. By extracting the gap signal characteristics of the experiment and operation data when the maglev train passes through the rail gap, the algorithm distinguishes the ideal rail gap and the rail step, with a gap compensation method further designed. The simulation results show that the proposed algorithm can effectively deal with the signal interference caused by the track steps, thus improving the stability of the suspension control system.