Maglev using EMS becomes unstable by unexpected big air-gap disturbance. The main causes of the unexpected air-gap disturbance are step-wise rail joint and large distance between rail splices. For the stable operation of the Maglev, the conventional system uses the threshold method, which selects one gap sensor among two gap sensors installed on the magnet to read the gap between magnet and guide rail. But the threshold method with a wide bandwidth makes the discontinuous air-gap signal at the rail joints because of the offset in air gap sensors and/or the step-wise rail joins. Further more, in the case of the one with a narrow bend-width, it makes Maglev system unstable because of frequent alternation. In this paper, a new method using fuzzy rule to reduce air-gap disturbances proposed to improve the stability of Maglev system. It treats the air-gap signal from dual gap sensors effectively to make continuous signal without air gap disturbance. Simulation and experiment results proved that the proposed scheme was effective to reduce air-gap disturbance from dual gap sensors in rail joints.