The distance between stations in the urban rail system is short, and trains start and stop frequently generating a large amount of regenerative braking energy. Formulating a reasonable charging and discharging strategy for the energy storage system (ESS) is of great significance for absorbing regenerative braking energy and achieving energy-saving effect. The ESS control strategy based on the train running state has more advantages than the existing strategies in terms of engineering realization and energy-saving effect. Due to the large amount of real-time detection information of the train running state and the complexity of engineering realization, this paper detects the output power of the substations and identifies the realtime cases based on the discrete Frechet algorithm to correct the train power. The ESS generates charge and discharge power reference values based on the real-time corrected train timetable. At the same time, the power distribution problem of the dual ESSs based on the train power following strategy is also considered, and a dual ESSs coordination strategy based on the dynamic proportional distribution of substation voltage is proposed. The example analysis verifies that this strategy is better than the fixed voltage threshold strategy. The energy-saving effect of the strategy is better.