The empirical model fails to capture the complex physical and chemical coupling processes occurring within the battery and the resulting response hysteresis, posing challenges for the development of precise control strategies for fuel cell systems. To address this issue, a control-oriented one-dimensional non-isothermal two-phase flow model was developed, with the transient effects of gas in the flow channel and the phase transition of water in the battery taken into account. The effects of current density on gas concentration and water-heat distribution characteristics were investigated. The impacts of operating conditions and model parameters on the output voltage of the battery were studied, and the advantages of the proposed model compared to the lumped parameter model in terms of output performance under current steps were analyzed. The results show that the model exhibits better applicability, providing a reliable foundation for model optimization and the design of control strategies at the fuel cell system level.