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Proton exchange membrane fuel cell (PEMFC) generates electricity through hydrogen and oxygen chemical reaction with the generation of much heat. According to the working temperature of PEMFC, the thermal resistance and internal relative pressure change of the flat-plate micro closed-loop pulsating heat pipe (CLPHP) are tested and analyzed at different filling ratios, vacuum degrees, and inclination angles, whose working medium is binary methanol-deionized water with a mass ratio of 5:1. The experiment results show that the higher the vacuum degree is, the better the startup and heat transfer performance of CLPHP become; the thermal resistance is less sensitive to inclination angle except for horizontal placement; the 40% volume-filling ratio can effectively avoid dry-out at high temperature. When 80 °C is the ideal working temperature of PEMFC, the thermal resistance of CLPHP is 0.093°C/W; the heat transfer heat flux is 1.59 W/cm², and the temperature fluctuation is small. Therefore, flat-plate CLPHP has great application potential for PEMFC cooling.