The ways to reduce rotor loss of a permanent magnet (PM) motor with 200kW/9000r/min for flywheel energy storage system (FESS) is discussed in this paper. Several methods are proposed to reduce the rotor loss by optimizing the structure of rotor. The air friction loss on the surface of rotor can be decreased rapidly when pressure in the sleeve is very small. So the rotor mostly works in a vacuum in high speed FESS. Due to the effect of time harmonics of stator current and space harmonics of air gap magnetic field, the loss in permanent magnets is considerable and leads to partial over-temperature. Thus the irreversible demagnetization of permanent magnets is occurred with poor cooling condition. The impact of rotor structure and silicon steel sheet thickness of rotor to the rotor loss are analyzed in the paper. The analysis and experimental results illustrate that there is the least rotor loss with the proposed rotor structures.