In this study, three imidazolium-based ionic liquids (ILs) and distilled water flushing were used to treat lignite subsamples to ascertain the inhibiting effect of ILs on the spontaneous combustion characteristics of lignite. The combustion characteristics, gas generation results during decomposition, and changes in the functional groups in these IL- and water-treated coal subsamples were compared with those of untreated coal through thermo-gravimetry and Fourier transform infrared spectroscopy analysis. The results showed that 1,3-dimethylimidazolium iodide ([Mmim][I]) was the most capable of reducing the -OH groups in lignite and inhibiting the spontaneous combustion of lignite. Furthermore, 1-ethyl-3-methylimidazolium iodide ([Emim][I]) was the most capable of increasing the -COOH groups in lignite and reducing the maximum mass loss rate of lignite. Analysis of the recovered ILs revealed that the ILs did not substantially change after the treatment, and recovery rates higher than 92% were achieved.