To explore the precise dynamic response of the levitation system with active controller, a maglev guide way-electromagnet-air spring-cabin coupled model is derived firstly. Based on the mathematical model, it shows that the inherent nonlinearity, inner coupling, misalignments between the sensors and actuators, load uncertainties and external disturbances are the main issues that should be solved in engineering. Under the assumptions that the loads and external disturbance are measurable, the backstepping module controller developed in this work can tackle the above problems effectively. In reality, the load is uncertain due to the additions of luggage and passengers, which will degrade the dynamic performance. A load estimation algorithm is introduced to track the actual load asymptotically and eliminate its influence by tuning the parameters of controller online. Furthermore, considering the external disturbances generated by crosswind, pulling motor and air springs, the extended state observer is employed to estimate and suppress the external disturbance. Finally, results of numerical simulations illustrating closed-loop performance are provided.