The AMB-rotor system is complex and has strong coupling characteristics, which allows multi-harmonic disturbances to enter the system through different ways to produce vibrations with rich spectrum components, which has a great influence on the improvement of micro-vibration accuracy of the rotor system. To further achieve active control of the micro-vibration in the AMB-rotor system, firstly, the mechanism of multi-source disturbance is analyzed according to the working principle of the AMB-rotor system, and the mathematical and physical relationship between the mechanism of disturbance generation and the inducement is deeply studied. Then, the structure of a novel adaptive notch filter, the method of adaptive frequency estimation and analysis of harmonic current suppression in the AMB system are presented. Finally, simulation and experimental research using an MSCMG system demonstrate the feasibility of the proposed method regarding the elimination of harmonic control current.