A dynamic decoupling control method based on neural network inverse system theory is developed for the 5 degrees of freedom (5-DOF) rotor system. The rotor system suspended by AC hybrid magnetic bearings (HMBs) is a multivariable, nonlinear and strong coupled system. Firstly, the configuration of 5-DOF HMBs and the mathematical equations of suspension forces are set up. Secondly, it is demonstrated the system is reversible by analyzing mathematical model. On the basis, the neural network inverse system which is composed of the static neural networks and integrators, and original system are in series to constitute pseudo linear systems. Finally, linear system theory is applied to these linearization subsystems for designing close-loop controllers. The simulation results show that this kind of control strategy can realize dynamic decoupling control, and control system obtains good dynamic and static performances.