This paper investigates the disturbance rejection problem of nonlinear MAGnetic LEViation (MAGLEV) suspension system with “mismatching” disturbances. Here “mismatching” refers to the disturbances that enter the system via different channel to the control input. The disturbance referring in this paper is mainly on load variation and unmodeled nonlinear dynamics. By linearizing the nonlinear MAGLEV suspension model, a linear state-space disturbance observer (DOB) is designed to estimate the lumped “mismatching” disturbances. A new disturbance compensation control method based on the estimate of DOB is proposed to solve the disturbance attenuation problem. The efficacy of the proposed approach for rejecting given disturbance is illustrated via simulations on realistic track input.