High seed design of flywheel and motor rotor is preferred to get higher energy and power density for the flywheel energy storage system. The rotor dynamics model of a composite flywheel storing energy of 25MJ driven by permanent magnetic motor with power of 400kW supported by active magnetic bearings running speed of 12000-24000rpm was built to reveal the natural frequencies and modes of the rotor bearing system. The rotor bearing system exhibited some flexible rotor dynamics performances such as shaft bending, local flexural structure mode and axial mode. Some modal frequencies varied sharply with the increase of rotational speed. The frequencies crossing and modes mixing are observed and described. The parameters such as bearing stiffness, core shaft structure and flexibility of coupling were analyzed and chosen to obtain a reasonable distribution for critical speed.