The battery inconsistency affects the lifetime of the battery, and the equalization management system can improve the battery inconsistency, but the present equalization management schemes cannot solve the battery inconsistency problem well. A two-layer distributed electric vehicle power battery equalization management system is proposed in this paper, and the equalization circuit is designed and the related control strategy is given. On the aspect of equalization circuit design, the two-layer distributed topology with top and bottom layers is designed. The coaxial multi-winding DC-DC converter is used to achieve energy transfer between the top-layer modules. The capacity and resistance equalizations are used to charge when the voltage between the cells in the bottom-layer modules is low, and discharge when the voltage is high. For the equalization control strategy design, the cell voltage, battery SOC and battery voltage dispersion are used to control the equalization process, and different equalization standards are selected according to different battery work states. Specially, during the discharge period, the electric vehicle running status is considered, and the voltage difference between the cells in the module is used to calculate the equalization step, and the equalization operation is conducted layer-by-layer and step-by-step. Finally, the resistance equalization system, the capacity equalization system and the two-layer distributed equalization system were tested on a battery with 12 cells. Before the equalization, the maximum voltage deviation among the cells was 90 mV. After two hours’ equalization operation, the maximum voltage deviation was reduced to 25 mV for the two-layer distributed equalization system, to 36 mV for the capacity equalization system and to 37 mV for the resistance equalization system. The test results indicate that the proposed equalization system has the highest equalization speed and efficiency.