With the large-scale development of new energy and the rapid growth of electric vehicles, battery energy storage systems can effectively promote the consumption of renewable energy and provide a cost recovery pathway for retired power batteries. However, most current research mainly focuses on using reconfigurable battery packs to flexibly switch the connection between batteries, in order to ensure the safe application of retired power batteries in energy storage systems, while neglecting further improvement of the overall energy storage life. Therefore, using the state of health (SOH) attenuation model, this article proposes a relationship function that links the available capacity of the energy storage system with the battery discharge rate and the discharge ampere-hour flux. Furthermore, a topology reconstruction strategy is proposed to ensure the maximum available capacity of the energy storage system, which is solved using the longitudinal and transverse cross algorithm. By comparing the overall capacity difference between reconfigurable energy storage systems and traditional energy storage systems under low-power demand through simulation, the effectiveness of the algorithm was verified, and the proposed strategy was demonstrated for optimizing the capacity of the energy storage system.