Maglev high-speed permanent magnet motor (M-HSPMM) has become a research hotspot of flywheel energy storage system due to its advantages of small size, high speed and high power density. However, vibration and noise have become the bottleneck restricting the development of flywheel energy storage system. In order to solve the above problems, the finite element method is used to analyze the electromagnetic performance of high speed permanent magnet motor used in flywheel energy storage system. On this basis, the expression of M-HSPMM radial electromagnetic force is analytically calculated, and its radial force wave property is studied. Further considering the influence of high temperature and thermal expansion, the interference quantity of the system is calculated and the stator mode is evaluated. Finally, the dynamic performance of M-HSPMM system, such as vibration response and noise is analyzed. The experimental results show that the electromagnetic noise has obvious order characteristics, which is mainly affected by the power supply frequency, carrier frequency and stator stiffness. It is found that the vibration noise of flywheel energy storage motor is mainly generated by 2 times frequency, and the interference quantity is proposed to reduce the vibration noise. After optimization, the vibration acceleration of vibration measurement point 1 is reduced from 4.23m/s2 to 1.61m/s2, and the noise value is reduced from 72.1dB to 65.5dB. Further research shows that the vibration response at 2 times frequency can be effectively reduced with the increase of carrier frequency. The above results can provide theoretical basis for the study of low vibration and low noise of maglev flywheel energy storage system.