In situ combustion (ISC) process has drawn more and more attention in the development of heavy oil reservoirs as a result of its high recovery efficiency. Although numerous studies have been reported that oil properties exhibit significant changes during the combustion process, the reaction mechanisms and evolution of oil components are still not well understood. In this work, the compounds of produced oils collected from a three-dimensional simulated production model (container) at different duration times after combustion being initiated and the original oil were characterized at the molecular level using gas chromatography (GC), gas chromatography–mass spectrometry (GC–MS), and high-field Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS). Both aromatic and acidic components were analyzed. The aromatic components showed relatively more stable characteristics than those of acidic components, and no obvious changes in aromatic compound distributions were observed by the positive ion atmospheric pressure photoionization (APPI) FT-ICR MS analysis. Small aliphatic acids were detected in the ISC oils, which were responsible for the high total acid numbers (TANs). The acidic Ox (x = 1–3) compounds, which have major contributions to the increase in TAN, were generated in greater abundances compared to that of the original crude oil. The carbon number distributions of the O1 and O2 classes in the produced oils significantly shifted to a lower carbon number region, with the dominant distribution from 15–40 at the initial state to 10–30 at the longest duration time. The double bond equivalent (DBE) values decreased during the combustion process. The generated acidic O1 components with DBE values less than 4 were also found in negative ion electrospray ionization (ESI) analysis, indicating the oxidation of hydrocarbons to alcohols.