In this paper, based on PI design principles for multivariate systems, a control system is designed that can meet the control requirements such as tracking velocity and regulating stator current with considering effects of suspension system on propulsion system. The dynamical model of linear synchronous motor with DC excitation used in the EMS maglev trains for propulsion is presented. In this system, the magnetizing inductances in the direction of the d and q axes are dependent on suspension air gap. So, by changing the suspension air gap from its desired value due to disturbances, these parameters change and consequently affect the performance of the motor, and the motor will be deviated from work point and the train will not follow its desired speed. The control system designed can compensate effects suspension system on propulsion system. Finally, the simulations confirm the performance of this controller.