The present invention relates to a design method of a grid energy storage system capacity in operation. For the problem of an energy storage system for power system secondary frequency modulation, a filter is used to distribute an AGC power command between a generator and an energy storage system, and with the minimization of the average daily cost of performing a frequency modulation task by the generator and the energy storage system as a target, the optimization model of a frequency modulation capacity is established. Through optimizing a filter parameter, the optimal frequency modulation capacity with lowest total average daily cost is obtained, and an optimal scheme is provided for energy storage system capacity configuration. The frequency modulation task is adjusted according to the respective frequency modulation ability of the generator and the energy storage system in operation. According to the strategy of adjusting the frequency modulation task of the energy storage system according to an energy storage system residual energy, the energy storage system residual energy can be maintained in a reasonable interval. The energy storage system participates in an AGC, the response ability of the whole system to an AGC power command can be greatly improved, and the climbing power of the generator is reduced.