To improve the anti-interference ability of maglev trains, a dynamic model of the high-speed maglev train with a nonlinear suspension controller for the guideway system is proposed in this paper. Based on the nonlinear characteristics of the magnetic suspension system, a nonlinear decoupling controller is designed using the feedback linearization theory. Then, a high-speed maglev train model is refined with a guideway coupling system, consisting of a maglev train simulated as a multi-body dynamics model with 537 degrees of freedom and a spatial finite element model of the guideway. Taking the Shanghai high-speed maglev train as an example, the correctness of the computational model is verified by comparing the modeling results with field measurement data, and the control effectiveness of the nonlinear controllers and the traditional PD controllers is compared considering different train speeds and disturbance forces. The results show that the suspension gap under the decoupling control is smaller than that under the PD control during the train operations. Under the same disturbance force, the decoupling control exhibits better control performance than the PD control. The variation amplitudes of the magnetic pole gaps are generally linearly related to the disturbance force.