Rational allocation of energy storage capacity is of great significance in suppressing the fluctuation of clean energy power and assisting frequency stability control of power grid. Aiming at the microgrid with wind and photovoltaic power generation, a primary and secondary frequency modulation model of energy storage system is established to take advantage of idle energy storage resources to participate in grid frequency modulation. Meanwhile,considering the power cost, investment and maintenance cost and other factors of the microgrid, the minimum daily comprehensive cost of the microgrid is the optimization goal. The equilibrium model among the microgrids is established based on cooperative game,and particle swarm optimization and interior point algorithm are used to solve the optimal capacity allocation of microgrids. The results of the example verify the rationality of the model and method.