The low speed maglev train which will be used in Badaling traveling line is regarded as the research object. On the basis of building the model of maglev control system and by analyzing the reciprocity between the maglev train and the rail, the designation of maglev train controller under the periodical irregularity of the rail is discussed. Two control schemes are also compared in this paper, one of which uses the relative displacement, the absolute velocity and the absolute acceleration as the feedback, the other uses the relative displacement, the relative velocity and the relative acceleration. The simulation results under different velocity and different bridge span are given in order to provide reference to the designation of the maglev control system and to the designation and construction of the rail track.