Frequent spontaneous combustion of coal is a major threat to coal mine safety. CO2 and N-2 are often used to prevent coal spontaneous combustion. To determine the differences between their reactions with coal, Fourier transform infrared spectroscopy ( FT-IR) was adopted to explore the functional groups distinction of coal samples oxidized in CO2/O-2 and N-2/O-2 atmospheres. The curve-fitting method and grey relational theory were selected to analyse the type, relative content and variation of major functional groups. The main functional groups in the samples were elucidated as oxygen-containing functional groups, aliphatic hydrocarbons and aromatic hydrocarbons. Oxygen-containing functional groups and aliphatic hydrocarbons are prone to react in low-temperature oxidation. As the oxygen concentration increased, hydroxy and CeO were continuously reduced. The aliphatic hydrocarbons content exhibited a significant decrease from the critical to crack temperatures in all atmospheres, indicating that they were extremely active in different oxidation stages. The effect of CO2 on inhibiting spontaneous combustion of coal was superior to that of N-2 when comparing the hydroxy contents in CO2/O-2 and N-2/O-2. Meanwhile, the results of the grey correlation analysis also verified this conclusion. The grey correlation grade cleared that hydroxy, C=O, aliphatic hydrocarbons and eCOOe were key functional groups relating to oxygen concentration. Their differences in the CO2/O-2 and N-2/O-2 atmospheres demonstrated that low-temperature oxidation of coal became slower under the influence of CO2 than N-2. The results from this study can clarify the difference between CO2 and N-2 in preventing coal spontaneous combustion from a micro view and provide a guide to selecting appropriate inhibitors in the goaf and working face.