The thermal decomposition of Nafion N117 membrane, a typical perfluorosulfonic acid membrane that is widely used in various chemical technologies, was investigated in this study. Structural identification of thermolysis products in water and methanol was performed using liquid chromatography-electrospray ionization-tandem mass spectrometry (LC/ESI-MS/MS). The fluoride release was studied using an ion-chromatography system, and the membrane thermal stability was characterized by thermogravimetric analysis. Notably, several types of perfluorinated compounds (PFCs) including perfluorocarboxylic acids were detected and identified. Based on these data, a thermolysis mechanism was proposed involving cleavage of both the polymer backbone and its side chains by attack of radical species. This is the first systematic report on the thermolysis products of Nafion by simulating its high-temperature operation and disposal process via incineration. The results of this study indicate that Nafion is a potential environmental source of PFCs, which have attracted growing interest and concern in recent years. Additionally, this study provides an analytical justification of the LC/ESI-MS/MS method for characterizing the degradation products of polymer electrolyte membranes. These identifications can substantially facilitate an understanding of their decomposition mechanisms and offer insight into the proper utilization and effective management on these membranes.