The motor is an important part of the flywheel energy storage system. The flywheel energy storage system realizes the absorption and release of electric energy through the motor, and the high-performance, low-loss, high-power, high-speed motors are key components to improve the energy conversion efficiency of energy storage flywheels. This paper analyzes the operating characteristics of the permanent magnet synchronous motor/generator (PMSG) used in the magnetically levitated flywheel energy storage system (FESS) and calculates the loss characteristics in the drive and power generation modes. Based on this, the electromagnetic part of the motor is optimized in detail. Aiming at this design, this paper calculates the loss characteristics of driving and power generation modes in detail, including its winding loss, core loss, rotor eddy current loss and mechanical loss. The calculation results show that the design meets the loss requirements. It can reduce the no-load loss of the permanent magnet synchronous motor at high speed and improve the energy conversion efficiency, which gives this system practical application prospects.