In view of the difficulties in adjusting new energy resources along electrified railways, uneven load distribution, and waste of potential energy in loading and unloading operations after trains arrive at stations, a design optimization strategy for the energy storage traction system of cross-regional freight railways is proposed. Analyzing the spatiotemporal characteristics of mobile energy storage charging and discharging, a time-sharing zoning electricity price model and an energy storage traction system capacity optimization allocation model were constructed to guide load time shifting to achieve peak shaving and valley filling in different time domains and geographical spans. It was proposed that an energy management strategy aiming at maximizing daily operating efficiency. The calculation example verifies that the designed energy storage traction system and its operation strategy can effectively improve the economic benefits during the operation cycle of the train, promote energy consumption along the line, and have important reference value for the low-carbon operation of electrified railways.