The invention provides an active power distribution system dynamic partition and energy storage device optimization configuration method and system. The method is characterized in that a distance between nodes is defined based on a voltage sensitivity factor; the dynamic partition information of an active power distribution system is given by utilizing the fast clustering algorithm based on peak density according to the above distance, a three-phase partition union at a certain period and the consideration degree and the compactness degree of partition nodes and an node importance index of betweenness of the three-phase partition union are solved to obtain the number and location of energy storage device configuration; a target function and constraints are defined to obtain the optimal capacity of the energy storage device. The method is advantaged in that the improved clustering algorithm based on peak density is utilized to solve the dynamic partition information of the active power distribution system, so the partition is made to adapt to changes in the way the system operates, the energy storage device is configured based on the partition information, and that the system has sufficient adjustment resources in each partition under each operation mode can be guaranteed.