Ketone compounds are oxidation products of crude oil in the in-situ combustion (ISC) process. Revealing the molecular composition of ketones can provide theoretical guidance for understanding the oxidation process of crude oil and valuable clues for studying the combustion state of crude oil in the reservoir. In this study, low-temperature oxidation (LTO) processes were simulated in thermal oxidation experiments to obtain thermally oxidized oil at different temperatures (170 °C, 220 °C, 270 °C, and 320 °C). A combination of chemical derivatization and positive-ion electrospray (ESI) Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) was used to analyze the molecular composition of different kinds of ketones (fatty ketones, naphthenic ketones, and aromatic ketones) in the oxidized oils at different temperatures. The results showed that the concentration of aliphatic ketones and aliphatic cyclic ketones in the product oils decreased with the increase in temperature, while aromatic ketones increased with the increase in temperature. At the same oxidation temperature, the content of ketones follows this order: fatty ketones < cycloalkanes < aromatic ketones. The concentrations of ketones reached their maximum value at 170 °C and decreased at high temperatures due to over-oxidation. It was also found that nitrogen-containing compounds are more easily oxidized to ketone compounds than their hydrocarbon counterparts in the LTO process.