A rotor supported by active magnetic bearing could offer various advantages over conventional bearings, but due to their limited force capacity, and moreover, the rotor has a mass unbalance. The vibration originated from the rotor's unbalance mass impacts on the dynamic properties, and even cause major accidents. Large unbalance is typically responsible for high energy vibrations and the consequent decrease in machine life. So unbalance compensation on the rotating machine is necessary, especially for the high speed flexible rotor. While the unbalanced vibration suppression need shutdown and phase sensor. To solve the problem of online suppress the unbalance vibration without adding additional hardware equipment in active magnetic bearing-rotor system, this paper proposes an online unbalanced vibration suppression based on the cross-correlation method and influence coefficient method. The amplitude and phase are achieved by cross-correlation method and feedback tracking control method in steady state. The active magnetic bearings are used to simulate the unbalanced excitation, the compensation amplitude of unbalance vibration signal are calculated by the influence coefficient method. The method was found to be effective and practical. An online test program was performed on a flexible rotor based on based on the Matlab/Simulink and a dSPACE real time system, which showed that the unbalanced vibration suppression could satisfy the performance and required precision of rotating machine, and the amplitude of the fundamental frequency of the unbalance vibration is significantly reduced.