The integration of renewable energy and hybrid energy storage system (HESS) into electrified railways to build electric railway smart microgrid system (ERSMS) is beneficial for reducing fossil fuel consumption and minimizing energy waste. However, the fluctuations of renewable energy generation and traction load challenge the energy management effectiveness for such a complex system. In this work, an energy management strategy is proposed which firstly decomposes the renewable energy into low-frequency and high-frequency components by an integrated empirical mode decomposition (IEMD). Then, a two-stage energy distribution approach is utilized to appropriately distribute the energy flow among the ERSMS. Finally, the feasibility and effectiveness of the proposed solution are validated through case study.