The application of new-designed levitation controller requires extensive validation prior to enter into commercial service. However, huge mounts of approximations and assumptions lead the theoretical analysis away from the engineering practice. The experimental methods are time-consuming and financial expensive, even unrealizable due to the lack of suitable sensors. Numerical simulations can bridge the gap between the theoretical analysis and experimental techniques. A complete overall dynamic model of maglev levitation system is derived in this work, which includes the simple-supported bridges, the calculation of electromagnetic force with more details, the stress of levitation modules and the cabin. Based on the aforementioned model, it shows that the inherent nonlinearity, inner coupling, misalignments between the sensors and actuators, and self-excited vibration are the main issues that should be considered during the design process of controller. Then, the backstepping controller based on the mathematical model of the module with reasonable simplifications is proposed, and the stability proofs are listed. To show the advantage of controller, two numerical simulation experiments are carried out. Finally, the results illustrating closed-loop performance are provided.