With the continuous acceleration of global urbanization, fossil energy is gradually depleting. Hydrogen energy is characterized by rich sources and low-carbon environmental protection. The use of hydrogen energy and fuel cells in rail transit is also one of the aspects to meet the country to promote green and low-carbon energy transformation. To ultimately enhance the overall economy of the fuel cell hybrid system in urban electric multiple units (EMUs), this paper would put forward an energy management strategy by focusing on the essence of minimum value, the minimum system hydrogen consumption as the objective, and then optimize the overall model of the system under the conditions of the state variable (lithium battery state of charge) and the control variable (the output power of fuel cell). Experimental results indicate that all performance metrics including the total amount of hydrogen consumed by the system, average efficiency of fuel cells have been improved substantially compared with the performance of the energy management strategy which is based on the state machine.