The wayside energy storage system has been widely used in the subway, but it cannot solve the “regeneration failure” problem. Therefore, an implement using onboard energy storage system to replace onboard braking resistor is proposed, which has the potential to eliminate the “regeneration failure” problem. This paper proposes a coordinated energy management strategy of onboard energy storage system. By receiving the charging threshold of the wayside energy storage system and the train power information, it has a better voltage stabilization effect and higher energy saving rate than the traditional energy management strategy. The feasibility and effectiveness of this strategy are verified by the simulation of actual subway lines.