Flywheel energy storage system (FESS) has the advantages of clean energy, high power, high efficiency, fast response and long service life, thus it has been widely used in various fields. In order to improve the speed and reduce the air friction loss, the rotor of FESS high speed permanent magnet synchronous motor (HSPMSM) operates at a magnetic suspension state in vacuum. It is very difficult for the rotor to dissipate heat, which even leads to demagnetization of PM. Moreover, the accurate analysis of HSPMSM rotor stress is essential. In this paper, a 200kW 20000r/min FESS HSPMSM is designed for uninterruptible power supply (UPS). From inside to outside, the composite rotor is composed of high strength alloy shaft, PM poles, nonmagnetic alloy sleeve, silicon steel sleeve and carbon fiber sleeve. Through the silicon steel sleeve, the eddy current loss induced by various alternating flux density harmonics in the rotor can be effectively suppressed, and the heat dissipation of HSPMSM rotor is solved fundamentally. Due to the carbon fiber sleeve and alloy sleeve, the mechanical strength of the composite rotor can be guaranteed. Then, through the finite-element analysis (FEA), the suppression of various flux density harmonics at the radial depth d(s) to the surface of the silicon steel sleeve is analyzed. The mechanical strength and electromagnetic performance of HSPMSM are analyzed to ensure the reliability of the composite rotor in high speed operation. The effectiveness of the designed motor is verified by simulation and experiment.