Centrifugal compressor is key equipment for process industry such as petroleum refinery and chemical. As the capacity and compress ratio as well as the efficiency increase, instability of rotor-bearing system become the major obstacle for it operation in a long period without shutdown. Based on the mechanism and affect factors research, the paper investigate the control strategy for improving the stability of rotor bearing system. After introducing a case study about a centrifugal compressor with several instable faults, transient response investigation is conducted to find the effect of rotating speed and cross coupling stiffness of seal on the stability of rotor. Then force can be exerted on rotor by controller through displacement feed-back or velocity feed-back strategy. By displacement feed-back, the controller functions as spring with cross-coupling stiffness opposite to seal. While, it function as a damper when velocity feed-back strategy is adopted. Results of the research indicate that both of the strategy can depress the vibration caused by instable of the rotor. Furthermore, displacement feed-back strategy has high efficiency because of it consume lower power. Results of this paper can provide new insight and feasibility for control or upgrade the stability of compressor rotor-bearing system.