At present, mobile communication devices are increasingly popularized all over the world, and there is an increasing demand for mobile power supply device. The main feature of the air-breathing proton exchange membrane fuel cell is that oxygen is only supplied via natural air breathing at its cathode without other active air supply equipment, thus making it conveniently portable. As a portable power supply device, it has great advantages in application, but its performance is inferior to traditional fuel cell because of its natural air intake. The products are now available on the market, but further design and improvement varies with the regional environment or other factors. A flexible tool capable of dealing with various conditions is necessary to save the experimental cost and optimize the cell. Regulation of the optimum cell design parameters with the trial-and-error method through experiment is time and resource-consuming. This study developed an air-breathing proton exchange membrane fuel cell that is time and resource-efficient, in the form of the computer simulation analysis. The main difference between the computer simulation analysis used in this paper and that in current studies is that the simulated cell is the real size without any geometrical simplification. Moreover, it can specifically reflect many detailed transport phenomena within the cell that cannot be seen via the traditional simplified model, so that the results are closer to the real phenomena. This study conducted experiment and simulation. The experimental method included design, manufacture, assembly, cell test and analysis. The physical phenomena that could not be measured by experiment were carried out with numerical simulation method. Physical phenomena, such as the pressure field, velocity field, concentration field, temperature field, ion conducting degree and current density, were observed in the cell. By observing the basic trend of the above physical quantities, such as pressure changes, speed, hydrogen concentration distribution and water concentration distribution in the anode, more oxygen consumption and more water generation in the cathode without water accumulation, all changes can be clearly controlled, so as to achieve the goal of optimizing the overall performance of the cell. The results of this study suggested that in the low temperature experiment, the low hydrogen flow rate leads to better cell performance; in the medium temperature experiment, the high hydrogen flow rate leads to better cell performance. Moreover, for the performance curve shown in experiments, the main cause of the performance difference can be investigated with the aid of the computer simulation analysis. The results showed that under the same humidification temperature, different hydrogen flow rates, different relative air humidity, and the increased hydrogen flow rate, the membrane material is dehydrated with decreased ion conducting degree, so that the overall performance decreased with the increase of the hydrogen flow rate. In addition, the detailed internal hydrogen concentration, air concentration, water concentration, pressure field, velocity field, relative air humidity, and current density distribution under different operating conditions were displayed by the computer simulation results.