The proton exchange membrane electrolysis cell (PEMEC) has attracted considerable attention for large-scale and efficient hydrogen production because of its high current density, high hydrogen purity and fast dynamic response. Flow field distributions and water and thermal management characteristics of a PEMEC are vital for electrolytic cell structure and the determination of operating condition. A three-dimensional, non-isothermal, electrochemical model of a PEMEC was established in this manuscript. The flow field distribution and water and thermal management of the PEMEC are discussed. The corresponding results showed that the pressure of the flow channel decreased diagonally from the inlet to the outlet, and the pressure and velocity distribution exhibited a downward opening shape of a parabola. At the same inlet flow rate, when the voltage was 1.6 V, the oxygen generation rate was 15.74 mol/(cm²·s), and when the voltage was 2.2 V, the oxygen generation rate was 332.05 mol/(cm²·s); due to the change in the oxygen production rate, the pressure difference at 2.2 V was 2.5 times than that at 1.6 V. When the stoichiometric number was less than two, the average temperature of the catalyst layer (CL) decreased rapidly with the increase in the water flow rate. When the voltage decreased to 2.1 V, the current density came to the highest value when the stoichiometric number was 0.7, then the current density decreased with an increase in the stoichiometric number. When stoichiometric numbers were higher than five, the surface temperature and current density remained basically stable with the increase in the water flow rate, and the water and thermal management and electrolysis characteristics performed better. The research results could optimize the water supply of electrolysis cells. According to the velocity distribution law of the flow field, the water and thermal management performance of the PEMEC could be estimated, further promoting safety and reliability.