Considering gyroscopic effect and flexibility of the shaft, the eight freedoms dynamic model is established. The dynamic characteristic and control quantity in different bearing rigidity and rotation axis are studied and discussed by optimal control theory. Furthermore, the controlling and the responding are discussed. The simulation results show that the bearing rigidity has great effect on the control quantity so that the elasticity of bearing must be considered. The asymmetry rigidity of rotational axis has little influence on stability. The conclusion may bring up theoretical references for precision control for rotor magnetic bearing system.