Synthetic hydrocarbon aviation lubricating oils (SHALOs) gradually degrade over time when subjected to high temperatures, resulting in their composition and properties varying over the operation lifetime. Therefore, understanding the SHALO degradation properties by elucidating the mechanism on a molecular level, as a function of high temperature, is of interest. A SHALO was subjected to thermal treatment (TT) at 180, 200, 230, 250, 270, or 300 °C for 2 h. The chemical compositions of six TT samples and one fresh oil were analyzed by fourier transform infrared F spectroscopy, advanced polymer chromatography, and gas chromatography/mass spectrometry. Furthermore, the physicochemical properties, such as kinematic viscosity, pour point, and acid number, of seven samples were determined. The oil samples were grouped by cluster analysis (CA) using a statistical method. The SHALO was identified to comprise 20 functional groups, including comb-like alkanes, long-chain diesters, amines, phenols, and other compounds. TT at <230 °C caused partial cracking of the SHALO base oils, with a concomitant change in the antioxidant content and type, and the polycondensation reactions were dominant. The observed antioxidant changes were not obvious from TT at >230 °C. A large number of small-molecule compounds were detected, including n-alkanes and olefins. TT at 250 °C was shown to be an important threshold for the kinematic viscosity, pour point, and acid number of the samples. Below 250 °C, the sample properties were relatively stable; but at elevated TT temperatures (>250 °C), the properties were observed to dramatically degrade. As the sample color was highly sensitive to temperature, the TT temperature induced rapid and significant color changes. The CA analysis results for the oil compounds at the molecular level were in good agreement with observed changes in the physicochemical properties at the macro level.