Proton exchange membrane fuel cell (PEMFC) is a complex system which involves multiple disciplines, and its output characteristics are affected by many factors. This paper aims to analyze the influences of working temperature, pressure, membrane water content, loading amplitude, and loading speed on its output characteristics. Based on the mathematical model of PEMFC, a voltage dynamic model that considers the electric double layer capacitance effect was established, and simulation was carried out on the Matlab/Simulink platform. Using the self-made air-cooled self-humidified DXFC-200 PEMFC and the fuel cell test system, the actual output volt-ampere curve was fitted to the model output curve, which proved the accuracy and stability of the model. On this basis, a longitudinal single-factor analysis was conducted. Besides, this study also conducted a multi-factor horizontal comparison by using an orthogonal experiment, and analyzed the impact of the operating temperature, pressure, and membrane water content on the output characteristics of the battery in low current region and high current region. Results show that the increase of the temperature, the pressure, and the water content of the membrane, and meanwhile decrease of the loading amplitude and the loading speed in a certain range could effectively improve the battery performance. In low current region, the operating temperature had a more important effect on the output characteristics of the battery. In high current region, the membrane moisture content had a more vital effect on the output characteristics of the battery. The research shows that the model can truly reflect the working characteristics of PEMFC. The study will provide theoretical support for improving battery performance, delaying battery attenuation and formulating fuel cell control strategy.