Coal spontaneous combustion (CSC) continues to generate huge economic losses and considerable casualties. Thew aim of this study is to further reveal the evolution of microstructures and coal spontaneous combustion mechanisms during natural oxidation. Coal samples with known CSC tendencies were selected to explore their microstructure and the characteristics of their reaction kinetics. This information is of great benefit to mine safety engineers and risk management professionals. Proper characterisation of risk leads to improved early warning detection, and the possibility of CSC retardant materials. A low-metamorphic type, non-caking coal sample was obtained from a Mengcun Coal Mine, and the relative content of the active functional groups and evolution of the key active groups were examined as temperature varied. Fourier transform infrared spectroscopy (FTIR) and the Coats-Redfern and Achar calculus methods were used to determine the reaction kinetics of the key active groups during CSC. The most probable mechanisms were determined, and the spontaneous combustion kinetic reaction mechanism was derived. Initial analysis of the sample revealed multiple active groups, active nuclear substances, a high calorific value, and a strong oxidative ability. There were a large number of oxygen containing functional groups and activity was high, due to the high intermolecular hydrogen bond content, and the apparent activation energy for ignition was low. Within the reaction, the aliphatic hydrocarbons were relatively stable; they had the largest apparent activation energy and were the least reactive. Methylene was the most important group consumed by aliphatic hydrocarbons in the CSC process. The reaction mechanism of the various groups were determined via Avrami-Erofeev equation. The large number of active groups produced and consumed was best described by the three-dimensional Ginstling-Brounshtein model.