To improve its performance, extend its lifetime, and overcome the problem of the slow dynamic during the start-up and the operation process of a proton exchange membrane fuel cell (PEMFC), this paper presents current short circuit and smart energy management approaches for a main PEMFC with auxiliary PEMFC, battery and supercapacitor as hybrid power source in parallel with an intelligent uninterrupted power supply (UPS) system. The hybrid UPS system consists of two low-cost 63-cell 300 W PEMFC stacks, 3-cell lead-acid battery, and 20-cell series-connected supercapacitors. Based on the designed intelligent hybrid UPS system, experimental tests and theoretical studies are conducted. Firstly, the modeling of PEMFC is obtained and evaluated. Then the performance improvement mechanism of the current short circuit is proposed and analyzed based on the Faradaic process and non-Faradaic process of electrochemical theory. Finally, the performances of the main PEMFC with the auxiliary PEMFC/battery/supercapacitor hybrid power source and intelligent energy management are experimentally measured and analyzed. The proposed current short circuit method can significantly extend the lifetime, improve the performance of PEMFC and decrease the size of the main FC for stationary, backup power sources and vehicular applications.