This paper proposes a capacity configuration method of the flywheel energy storage system (FESS) in fast charging station (FCS). Firstly, the load current compensation and speed feedback control (LCC-SFC) strategy adopted by permanent magnet synchronous motor (PMSM) is introduced and the curve of “source-storage-load power characteristics” is obtained. Then, the capacity configuration of PMSM-FESS that satisfies the load energy and power requirements in the initial stage of fast charging is studied, which includes the rotational inertia of flywheel rotor and the mechanical angular velocity. Also, the power allocation of flywheel-side converter is analyzed. Finally, the system simulation model is built under Matlab/Simulink, the simulation value of the slope of gird power is approximate to its theoretical expected value. And the effectiveness of the capacity configuration method is verified. The results are helpful to the practical application of PMSM-FESS in the field of EV fast charging station.