An air-breathing polymer electrolyte membrane fuel cell bears many advantages, which are important for portable-power applications. However, several barriers must be overcome before an air-breathing PEMFC achieve commercially wide-scale adoption. In this paper, with emphasis on improving the performance of air-breathing PEMFC, the simulation and experiment has been done simultaneously. Considering the natural convection in the cathode side, electrochemical reaction in the catalyst layer, water transport in the membrane, a coupled three-dimensional complex model has been developed in this work. The parameters which greatly affect the performance of an air-breathing PEMFC have been calculated for the base case such as the distribution of water and reactant, temperature and electrochemical performance. To validate the numerical result, the experiment test system have been designed to investigate the temperature distribution and cell performance. The results from this work show that the performance of air-breathing PEMFCs is strongly affected by natural convection feature. The concentration losses play a major role on the cell performance. The ambient relative humidity also has significant effect on the cell performance. The fields of water, temperature, velocity and electrochemical reaction have strong interaction on each others.