The performance of the Flywheel Energy Storage System (FESS) is excellent when it is applied on the adjustment of the grid frequency. FESS can improve the stability of the grid frequency and guarantee the reliability and stability of the grid. In order to enhance the system performance and rotation speed accuracy during the charge process of FESS with Permanent Magnet Synchronous Motor (PMSM) under grid vibration, this paper proposes the Adaptive Robust Control (ARC) method and the continuous reference curve of the rotor rotation speed to reduce the system vibration and impact based on the vector control strategy. The developed methods are verified through the built simulation model. Then it applies the PID control method and the uniform acceleration reference curve of the rotation speed on the FESS. The simulation results show that the steady state speed error is 0.03% and the steady state error of the angular acceleration is 0.7% for the system with ARC method and the continuous reference curve, while the maximum speed error is 0.8% under the grid vibration. For the system with PID method and the uniform acceleration reference curve, the steady state speed error is 0.08% and the steady state error of the angular acceleration is 1.6%, while the maximum speed error is 6.0% under the grid vibration. Therefore, the FESS with ARC method and continuous reference curve owns much better performance and rotation speed tracking accuracy than the system with PID method and the uniform acceleration reference curve during the charge process. This work is supported by National Key Research and Development Program of China (No. 2017YFC0805905), National Natural Science Foundation of China (No. 51775186) and Fundamental Research Funds for the Central Universities in China (No. 2017MS074).