For magnetically suspended rigid rotors (MSRs) with significant gyroscopic effects, phase lag of the control channel is the main factor influencing the system nutation stability and decoupling performance. At first, this paper proves that the phase lag of the cross channel instead of the decentralized channel is often the main factor influencing the system nutation stability at high speeds. Then a modified cross feedback control strategy based on the phase compensation of cross channel is proposed to improve the stability and decoupling performances. The common issues associated with the traditional control methods have been successfully resolved by this method. Analysis, simulation, and experimental results are presented to demonstrate the feasibility and superiority of the proposed control method.