The empirical model cannot reflect the complex physical and chemical coupling process inside the battery and the resulting response hysteresis, which brings certain difficulties to the development of precise control strategies for fuel cell systems. Aiming at this problem, a control-oriented one-dimensional non-isothermal two-phase flow model was established. The transient effect of gas in the flow channel and the phase transition of water in the battery were considered, and the influence of current density on gas concentration and water-heat distribution characteristics was studied. The influence of operating conditions and model parameters on the output voltage of the battery was investigated, and the advantages of the model compared with the lumped parameter model in terms of output performance under the current step were explored. The results show that the model has better applicability and can provide a reliable basis for model optimization and control strategy design at the fuel cell system level.