Abstract: Aiming at the problems in the power grid such as the difference in frequency modulation (FM) cost and residual FM capacity of different types of battery energy storage power stations (BESPSs), and the state of charge (SOC) of battery energy storage units (BESUs) in BESPSs could be too high or too low, a two-layer optimization strategy which takes FM cost and SOC recovery into account in multi-battery energy storage system was proposed. The strategy includes FM power optimization layer and SOC optimization layer. In the FM power optimization layer, the resistance coefficient related to the residual FM capacity of the BESPS was introduced. The objective function of this layer was composed of resistance coefficient and FM cost, so that the optimal distribution of FM power between different BESPSs can be realized according to the FM cost and residual frequency modulation capacity of different BESPSs. The SOC weight was introduced in the SOC optimization layer which can reallocate the FM power of different BESPSs to recover the SOC of BESUs. A regional power grid with three different battery types was used to verify the effectiveness of the proposed strategy. The results show that compared with the three contrast strategies, the proposed strategy not only has better economic benefits, but also can restore the SOC of BESUs and improve the FM effect of BESPSs.