The invention discloses a layered equalizing circuit system based on a series battery stack and a hybrid control method, and belongs to the technical field of battery energy storage systems. A bottom layer of the architecture adopts an adjacent cell-cell (C2C) structure, and is divided into different battery packs. A top layer adopts a transformer coupled multi-directional multi-port converter, and bidirectional energy flow among arbitrary battery packs of the bottom layer is realized. The layered architecture can reduce the amount of equalizing circuits working simultaneously, so that the repeated charging and discharging problem of the batteries in the equalizing process is avoided, and the health status of the batteries is improved. According to the hybrid control method, during the standing of the batteries, the equalizing current required for each battery cell is obtained by calculating SOC, so that an equalizing system is controlled; when the batteries work, each equalizing circuit is controlled by calculating SOC change rate, so that a potential unequalizing tendency is forecasted in advance and is corrected, and real-time equalizing for each battery is guaranteed. Moreover, according to the layered architecture and the control method, the rated current required for the equalizing circuit can be reduced, so that the system cost is reduced, and the energy loss is reduced.