The invention relates to a double-layer hierarchical optimization configuration method of an energy storage system in an active power distribution network. The double-layer hierarchical optimization configuration method comprises the steps of building an outer-layer planning model, wherein total investment cost is taken as a target, year is taken as minimum planning unit, and optimization objects are installation position and installation capacity of the energy storage system; and building an inner-layer running model, wherein optimal running economy is taken as a target, day/hour/minute is taken as minimum running unit, and an optimization object is a running control variable of storage energy. An optimal solution of the outer-layer planning model is figured out by mutual relation between the inner-layer running model and the outer-layer planning model, and optimization configuration of the energy storage system in the active power distribution network is further achieved. With regard to unfavorable influence of a distributed power supply on the power distribution network, two different time scale problems of running control and planning design are combined, so that the configuration of the energy storage system can be reasonably optimized, and the economy of the power distribution network is improved.