A three-dimensional (3D) model has been developed to simulate proton exchange membrane fuel cells. The model accounts simultaneously for electrochemical kinetics, current distribution, hydrodynamics, and multi-components transport. A single set of conservation equations of mass, momentum, energy, species, and electric current are developed and numerically solved using a finite-volume-based computational fluid dynamics technique (by computational fluid dynamics commercial code). The physical model is presented for a 3D geometry test cell with serpentine channels and counter flow. Subsequently, the model is applied to explore cell temperature effects in the cell environment with different relative humidity of inlet. The numerical model is validated and agreed well with the experimental data. The nonuniformity of thermal and water-saturation distributions is calculated and analyzed as well as its influence on the cell performance. As the cell is operated at low voltages (or high current densities), the thermal field of fuel cell tends to be nonuniform and exists locally in hot spots. The mechanism of thermal field and water content interacted with membrane dehydration and cathode water flooding will be discussed and revealed their influences on the cell performance, stability and degradation will be revealed.