A reduced-order model (ROM) is developed for proton exchange membrane fuel cells (PEMFCs) considering the non-isothermal two-phase effects, with the goal of enhancing computational efficiency and thus accelerating fuel cell design development. Using analytical order reduction and approximation methods, the fluxes and source terms in conventional 1D conservation equations are reduced to six computing nodes at the interfaces between each cell component. The errors associated with order reduction are minimized by introducing new approximation methods for the potential distribution, the transport properties, and the membrane hydration status. The trade-off between model accuracy and computational efficiency is studied by comparing the simulation results and computational times of the new model with a full 1D model. The new model is nearly two orders of magnitude faster without sacrificing too much accuracy (<4% difference) compared to the 1D model. The new model is then used to analyze the influence of the membrane electrode assembly (MEA) design on cell performance and internal state distributions, offering insights into MEA structural optimization. The model can be readily extended to account for more detailed physico-chemical processes, such as Knudsen diffusion or the influence of micro-porous layers, and it can be an effective tool for understanding and designing PEMFCs.