Track irregularity is one of the most important aspects of the suspension control performance impact in Magnetic Transportation System (MTS). By using the traditional PID control, the problem was that it was difficult to confirm the PID parameters and have long settling time, even appear the chaotic phenomenon. However, using Expert PID(EPID) control method producesd over-fitting to initial assignments, local optimum induced easily and slow convergence rate problem. Based on the global optimization feature of PSO algorithm, it had been adopted to optimize the initial values of Expert PID control. An intelligent control algorithm for the maglev transportation system was put forward based on Expert PID optimized by Particle Swarm Optimization algorithm (EPID-PSO). The expert rule was that if the absolute value of the error trended to decrease, the PID current control keeped its maintenance; if not, then the PID current control applied strong functions. Under this rule, the dynamic error was reduced and the performance of track irregularity was improved. Simulation results by MATLAB proves that the control scheme has good robustness, shorter adjustment time, faster response time, achieving better quality of control under the three conditions of step signal, low frequence sine wave signal and high frequence square wave signal.