To investigate the biogas generation characteristics of the organic matter in lignite, methanol extraction was conducted to obtain the soluble fraction and the residual of lignite, which were subsequently taken as the sole carbon source for biogas production by a methanogenic consortium. Afterward, the composition of compounds before and after the fermentation was characterized by UV-Vis, GC-MS, and HPLC-MS analysis. The results indicated that the methanogenic microorganisms could produce H2 and CO2 without accumulating CH4 by utilizing the extract, and the methane production of the residue was 18% larger than that of raw lignite, reaching 1.03 mmol/g. Moreover, the organic compounds in the methanol extract were degraded and their molecular weight was reduced. Compounds such as 1, 6-dimethyl-4-(2-methylethyl) naphthalene, 7-butyl-1-hexylnaphthalene, simonellite, and retene were completely degraded by microorganisms. In addition, both aromatic and non-aromatic metabolites produced in the biodegradation were detected, some of which may have a negative effect on the methanogenesis process. These results revealed the complexity of the interaction between coal and organism from another point of view.