The disclosure relates to a flywheel energy storage system including a casing, shaft, flywheel, and electric motor assembly. The casing has an inner vacuum chamber, at least one outer accommodating slot and at least one separator which separates the inner vacuum chamber from the at least one outer accommodating slot. The shaft is rotatably disposed in the inner vacuum chamber. The flywheel is located in the inner vacuum chamber and fixed to the shaft. The electric motor assembly includes a first motor rotor and a motor stator. The motor stator is accommodated in the at least one outer accommodating slot and fixed to the at least one separator. The first motor rotor is fixed on the shaft and located between the shaft and the motor stator. Part of the at least one separator located between the first motor rotor and the motor stator includes magnetically permeable material.