While proton exchange membrane fuel cell (PEMFC) generates electricity, about half of the energy is converted into heat. According to structural characteristics and heat dissipation requirements of PEMFC, a flat-plate micro closed-loop pulsating heat pipe (CLPHP) cooling method is designed. The flat-plate CLPHP is an aluminum alloy plate with a thickness of 2.4 mm, and the inside is a 2.3 mm x 1.4 mm rectangular flow channel, which transfers heat mainly through the internal working fluids vapor-liquid phase change and forced convection. The experiment tested the heat transfer performance and the internal pressure of pure working fluids methanol, ethanol, isopropanol, deionized water, and methanol-deionized water with different mass ratios. By comparison, it is found that the binary working medium methanol-deionized water with a mass ratio of 5:1 has the best startup performance, lower internal pressure, and less temperature fluctuation, which has great potential in the application of PEMFC. Through the dimensionless number correlation analysis of the internal working fluids thermophysical parameters, a CLPHP heat flux prediction equation with an average deviation of 15.0% is fitted. (c) 2021 Hydrogen Energy Publications LLC. Published by Elsevier Ltd. All rights reserved.