The deployment of wayside energy storage systems (WESSs) in substations is a key strategy for enhancing the energy efficiency of urban rail transit (URT). Existing research on energy management in traction power system (TPS) with WESS primarily focuses on improving the utilization of surplus regenerative braking energy in the system. However, due to the ambiguous output characteristics of TPS with WESS, it is challenging to address the optimization of overall system energy consumption from the perspective of power flow control, marking a significant distinction from flexible traction power systems (FTPSs) based on bidirectional substations. To address this issue, this paper proposes an integrated energy storage substation (IESS) control method and develops a steady-state equivalent model along with a DC power flow model for TPS with IESSs. Furthermore, under the framework of optimal power flow, this paper achieves both optimized control and flexible power supply for the TPS with IESS. Simulation results based on real-world operation scenarios demonstrate that the proposed method effectively optimizes the TPS power flow and reduces the total system energy consumption, offering new insights into the construction of FTPS based on the IESS.