The power imbalance between the source and the load in the microgrid system will cause frequency fluctuations. In this paper, a fuzzy adaptive frequency control strategy based on flywheel energy storage system (FESS) is proposed to suppress the microgrid frequency fluctuation. Firstly, a frequency control strategy is designed based on fuzzy control. The fuzzy control takes into account the frequency deviation of microgrid system and the energy state of the FESS for the design of fuzzy rules, so that the FESS can carry out adaptive frequency control according to the microgrid frequency change situation and the energy state of the FESS. Secondly, the voltage control strategy is designed to obtain the reference value of machine-side power of the FESS by compensating the bus capacitance energy and the loss of FESS, to improve the speed of power balance of the FESS and reduce the fluctuation of the bus voltage. Finally, the correctness and effectiveness of the proposed control strategy are verified by simulation.