The composite material flywheel rotor of a flywheel energy storage system (FESS) has a low natural frequency. When the system suffers from noise interference, the magnetic bearing generates a force with the same frequency as the natural frequency and causes vibration to occur. Thus, it is necessary to suppress the natural vibration of the magnetic suspended (MS) FESS. The LMS adaptive notch filter is generally adopted for vibration suppression. The vibration suppression performance of the system is different when the insertion position of the notch filter is different. This paper analyzes the influence of the notch filter in different insertion positions of the control system. Through the transfer function from noise to magnetic bearing force, theoretical analysis of the influence of different positions of the notch filter is performed. Corresponding experiments are performed in a 500 kW MS FESS prototype. The theoretical analysis is verified experimentally.