In this article, two kinds of perfluoropolyether (PFPE) with different terminal groups were investigated using thermogravimetric analysis (TGA), infrared (IR) spectroscopy, gel permeation chromatography (GPC), and gas chromatography/gas mass spectrum (GC/MS) analysis. PFPEs with a hydroxyl or carboxylic acid terminal group were more heat stable than was PFPE with carboxylic methyl ester. Perfluoropropylene oxide-type PFPE with a perfluoroethyl terminal group at one end tends to lose weight more rapidly than does copolymer-type PFPE with dihydroxyl or dicarboxyl methyl ester terminal groups at both ends. The residual weight fraction of PFPE with a perfluoroethyl terminal group was dependent on the average molecular weight. The number-average molecular weight of PFPE can be calculated from the peak intensity ratio between the polar group and C-F stretching by measuring the IR spectrum of PFPE. The number-average molecular weight of PFPE increased because of the evaporation loss of its low molecular weight fraction and the crosslinking reaction of PFPE with increase in temperature. GC/MS analysis showed that the main product of the pyrolysis of PFPE was hexafluoropropylene. We speculated on the PFPE degradation mechanism and the optimum PFPE chemical structure in terms of heat stability.