The suspension system of the maglev train is a complex system, which is difficult to model accurately. The horizontal misalignment between the suspension magnet and the rail is one of the common uncertainty factors in the suspension system, which will affect the suspension performance. This article focuses on this problem. Firstly, the formula of suspension force considering horizontal misalignment is derived and the results of the formula and the FEA (Finite Element Analysis) simulation is consistent. Secondly, a suspension system model considering the horizontal misalignment is established for the first time, which can effectively describe the impact of the horizontal misalignment on the suspension system. Thirdly, a controller for the suspension system is designed by using the GIMC (Generalized Internal Model Control) paradigm and how the controller can effectively suppress the uncertainty caused by the horizontal misalignment is proved theoretically for the first time. Finally, the simulation and physical experiment verify that the proposed algorithm shows excellent performance and robustness in the system.