Aiming at the problems of low frequency regulation efficiency and insufficient capacity in modern power system, a two-layer frequency regulation control strategy considering the difference between frequency regulation energy consumption and energy storage state of charge (SOC) is proposed. The frequency regulation method of distributed energy storage based on aggregation method is introduced to simplify the solution variables of secondary frequency regulation, and a two-layer frequency regulation control strategy is proposed, which takes into account the economic distribution of energy storage power and the difference of SOC, and realizes the effective management of frequency regulation output of distributed energy storage units. The simulation results show that the frequency modulation deviation of the distributed energy storage frequency modulation strategy divided according to the energy storage type is low. The maximum frequency deviation of this strategy is only 0.125 Hz, the frequency sliding speed is only 1.26×10-3 Hz/s, and the frequency recovery speed is up to 58.91×10-6 Hz/s. The root mean square error between the state of charge and 0.5 is only 0.85, which is 0.39 less than strategy of frequency modulation by directly solving the energy consumption function of frequency modulation. This strategy has high frequency modulation efficiency and low energy consumption.