Proton exchange membrane water electrolyzer (PEMWE) is the promising approaches for the sustainable development of energy. The mass and heat transfer directly affects the cell performance at high current density, and transfer characteristics are currently unclear due to the complex reaction process. It is important to develop the detailed modeling and investigate the characteristic distribution to achieve future performance optimization. Therefore, a three-dimensional full-scale two-phase model, which couples fluid dynamics, electrochemical reaction kinetics, heat- and mass- transfers, and two-phase flow, is developed for a PEMWE. The model accuracy is validated by experimentation. Subsequently, the effects of the crucial operating and structural parameters on the cell characteristics are investigated. Furthermore, a theoretical analysis is conducted to evaluate the impacts of these parameters on energy efficiency. Results suggest that the cell performance depended strongly on the increased working temperature, the maximum current density is increased by up to 80.55 % at 2.3 V with the rise in working temperature, leading to a corresponding aggravation in gas accumulation. The flow rate of liquid water plays a positive role with regard to reducing the temperature difference of membrane and accelerating gas discharge. In addition, the channel sizes improve the cell performance within limits, wherein the increased channel width significantly contributes to reduction in mass transfer resistance of fluid between the channel and the diffusion layer. Furthermore, the energy efficiency depends on the electrochemical reaction rate the channel width and depth of 1.5 mm can effectively improve cell performance and energy efficiency, while balancing trade-off between gas accumulation and mass transfer resistance. This study offers a reference for further mechanism analysis of PEMWE, and lays a foundation for optimizing performance via characteristic distribution and energy efficiency.