The large-scale new energy sources such as solar and wind energy bring challenges to system frequency regulation. With the recognition of new energy storage as an independent market entity, it is necessary to study how independent energy storage can participate in automatic generation control (AGC) command mode and control with other generators. Firstly, this paper introduces the regulation range, upper and lower regulation characteristics, and requirements of energy storage and conventional units. Secondly, the AGC control unit’s response curve to AGC instructions is reasonably simplified for calculating benefits for each entity. Then, the AGC command distribution method based on the available frequency regulation capacity is established, and an AGC control mode suitable for independent energy storage power stations is proposed to maximize the frequency regulation mileage revenue. Finally, based on three typical AGC scenarios: continuous down regulation response, continuous up regulation response, and fluctuation of up and down regulation response, four schemes—only conventional units, priority call for independent energy storage, call for energy storage based on available frequency regulation capacity, and joint frequency regulation are compared, verifying the effectiveness of the model proposed.