With the rapid increase in the proportion of wind power, the frequency stability problem of power system is becoming increasingly serious. Based on MATLAB/Simulink simulation, the role and effect of secondary frequency modulation assisted by Flywheel Energy Storage System (FESS) in regional power grid with certain wind power penetration rates are studied. First, the linear frequency control of the power system is used to establish the primary frequency modulation control model of FESS assisting wind power, and the frequency characteristics of FESS participating in primary frequency modulation are analyzed according to the transfer function. Then, in the case of step disturbance and continuous disturbance of load power, the frequency characteristics of a regional power grid are simulated and demonstrated through time domain simulation, and conclusions are drawn through comparison; a certain proportion of FESS can quickly respond to the frequency deviation signal. During secondary frequency modulation simulation, the maximum frequency deviation of the system is reduced by 57.1% and the frequency fluctuation range is reduced by 53.8%, effectively improving the frequency quality of the power grid.