In this paper, an advanced teaching-learning based optimization(TLBO) method for the magnetic levitation controller of Maglev transportation system is proposed to optimize the control performances. An attraction-type levitation system is intrinsically unstable and requires a delicate control. It is difficult to completely satisfy the desired performance through the methods using conventional methods and intelligent optimizations. In the paper, we use TLBO and clonal selection algorithm to choose the optimal control parameters for the magnetic levitation controller. To verify the proposed algorithm, we compare control performances of the proposed method with the genetic algorithm and the particle swarm optimization. The simulation results show that the proposed method is more effective than conventional methods.