The invention discloses a multi-level active equalization circuit of an energy storage battery system and a control method thereof. A battery energy storage system is divided into a plurality of modules by adopting a multi-level active equalization structure; wherein the active equalization circuit comprises an intra-group equalization circuit and an inter-group equalization circuit, the intra-group equalization circuit comprises a battery state information acquisition circuit, an intra-group switch array, an intra-group bidirectional DC-DC circuit and a slave MCU, and the inter-group equalization circuit comprises an inter-group switch array, an inter-group bidirectional DC-DC circuit and a master MCU; intra-module equalization is achieved through active equalization in the modules, and equalization between the modules is achieved through adoption of the module equalization main circuit. Effective utilization of energy in the energy storage battery system can be achieved, the overallcapacity and the power performance of the battery pack can be effectively improved, and meanwhile, the equalization time is shortened.