[Objective] The flux switching linear motor (FSLM) magnetic levitation system is a nonlinear, strongly coupled, parameter time-varying system. Due to the lack of an intermediate transmission device in the FSLM, combined with external disturbances and the inherent end effects of the linear motor, controlling the magnetic levitation system becomes more challenging. To improve the control performance of the magnetic levitation system, an interval type-2 fuzzy super-twisting sliding mode control (IT-2FSTSMC) strategy is proposed. [Methods] Firstly, the mathematical model of the magnetic levitation system was established according to the structural characteristics and operating principle of FSLM. A nonlinear coordinate transformation was applied to derive an affine nonlinear mathematical model of the FSLM magnetic levitation system. Secondly, a new integral sliding mode surface was designed, which could adaptively regulate the convergence rate of the state variables, thereby improving the system’s response perform