Abstract: The electrolyte volume fraction in agglomerate and the agglomerate radius in the cathode catalyst layer of a proton exchange membrane fuel cell affect the oxygen transport resistance, which affects the electrochemical reaction rate, as well as the heat generation and transfer in the fuel cell. However, the effects of electrolyte volume fraction and agglomerate radius on heat transfer in a fuel cell are not clear. Therefore, in this paper, a two-dimensional, two-phase, non-isothermal proton exchange membrane fuel cell agglomerate model is established to investigate the effects of electrolyte volume fraction and agglomerate radius on temperature distribution and heat production in a fuel cell. Results show that the increase of electrolyte volume fraction and the decrease of agglomerate radius are beneficial to the decrease of the oxygen transport resistance, the improvement of cell performance, the increase of the heat production of each part of the membrane electrode assembly, and the increase of the heat production of oxygen reduction reaction, ohmic heat production and the heat production of phase change of water in the cathode catalyst layer, while they are not conducive to the uniform distribution of temperature.