To better compensate for the voltage drop of DC-side bus in an electric vehicle (EV) fast charging station and limit the power ramp rate of power grid, a nonlinear control strategy of flywheel energy storage system for the DC fast charging station is proposed based on the immersion and invariance theory. First, considering the power balance relationship of the power supply system in the fast charging station, the impact characteristics caused by the charging load instantaneous access under the traditional control strategy of flywheel energy storage system are analyzed, and the voltage stability of DC-side bus is determined as the optimization objective. Then, the effect of bus voltage control and the control accuracy of energy storage output current are considered, an affine nonlinear model of flywheel energy storage is established, the manifold surface and control law are constructed using the immersion and invariance method to provide the capability to quickly respond to the charging load current mutation and flywheel speed change, and a charging and discharging control strategy for the energy storage system is designed. Finally, a simulation model is built to compare and analyze different control strategies under single-and multi-EV access, and results show that the proposed control strategy can effectively suppress the influence of electric vehicle access and flywheel speed change on the bus voltage, thereby alleviating the impact on the distribution network.