To suppress multi -frequency harmonic vibration caused by displacement sensor runout in a magnetic suspension flywheel system, an adaptive variable step-size least mean square ( LMS) algorithm is proposed. The model is established to identify the displacement stiffness coefficient κh and current stiffness coefficient κi of the magnetic bearing rotor. The octave frequency noise caused by the displacement sensor runout is taken as the suppression target. On the basis of the adaptive LMS algorithm, a modified variable step-size factor with changing frequency is improved to achieve automatic balancing. The stability of close loop system is analyzed by general?ized root locus. Simulation results show that the proposed method can effectively suppress octave frequency dis?turbance.