A two dimensional, across the channel, steady-state model for a proton exchange membrane fuel cell (PEMFC) is presented in which the non-isothermal model for temperature distribution, the two-phase flow model for liquid water transport and the agglomerate model for oxygen reduction reaction are fully coupled. This model is used to investigate thermal transport within the membrane electrode assembly (MEA) associated with the combinational water phase-transfer and transport mechanisms. Effective temperature distribution strategies are established aim to enhance the cell performance. Agglomerate assumption is adopted in which the ionomer and liquid water in turn cover the agglomerate to form the ionomer and liquid water films. Ionomer swelling is associated with the non-uniform distribution of the water content. The modelling results show that heat accumulates within the cathode catalyst layer under the channel. Higher operating temperature improves the cell performance by increasing the kinetics, reducing the liquid water saturation on the cathode and increasing the water carrying capacity of the anode gas. Applying higher temperature on the anode and enlarging the width ratio of the channel/rib could improve the cell performance. Higher cathode temperature decreases the oxygen mole fraction, resulting in an insufficient oxygen supply and a limitation of the cell performance.