The influence of calcite on the spontaneous combustion of coal was investigated at macroscopic and atomic levels. Experiments on raw coal and coal with 2%, 5%, and 8% calcite included programmed temperature tests, thermogravimetric (TG) analysis, specific surface area measurements, and in-situ infrared spectroscopy. Ultimate analysis, C-13 NMR, and X-ray photoelectron spectroscopy (XPS) experiments facilitated the development of a coal molecular model, with molecular dynamics simulations based on reactive force-field (ReaxFF). The presence of calcite considerably reduced CO and CO2 production during the coal-oxygen reaction compared with untreated coal. Calcite incorporation increased the characteristic temperature points and activation energy of the coal-oxygen reaction, reducing the risk of spontaneous combustion. The addition of calcite reduces the specific surface area and decreases the content of active functional groups, thereby passivating the oxidation of active groups such as -CH3 and -OH. ReaxFF simulations indicated that the addition of calcite suppressed light and heavy tar formation, decreased oxygen consumption, slowed down the coal-oxygen reaction, and reduced major gaseous products (e.g., CO, CO2 and CH4), consistent with the experimental results. Potential energy analysis revealed that calcite lowered the potential energy of coal-oxygen reaction, thereby enhancing stability of coal and reducing its reactivity. The generation pathways of CO and CO2 showed that coal oxidation starts with pyrolysis, with untreated coal having more reaction sites than coal with calcite.