Abstract: Kaolinite is a common mineral in coal, and its influence on the metabolic process of coal biological methane is less concerned. In this study, lignite and kaolin after demineralization were selected to explore the control effect of kaolin on coal bio-gas production through bio-gas production simulation experiment, infrared spectrum analysis, XPS, fluorescence spectrum and metagenomic analysis. The results show that adding a certain proportion of kaolin can effectively promote the production of biological methane. Among them, adding 6% kaolin, the biological gas production increased by 90.4% compared with the raw coal, and excessive kaolin will inhibit the production of biological methane. Kaolin made the macromolecular structure of coal in the fermentation system change more obviously, and aromatic substances were effectively converted into small molecular weight substances. The fermentation system with kaolin addition further oxidized phenolic carbon or ether carbon in coal samples to organic acids, and the relative contents of C—C and C—H decreased by 2.01% and 10.20%, respectively. Soluble organic matter can be effectively degraded and utilized, which is conducive to biogas production. Kaolin promoted the increase of microbial flora species abundance, enhanced the gene abundance of key enzymes in each methanogenic pathway, and promoted the degradation of various complex substances in the fermentation broth and the conversion of methane. The research results provide experimental support for the influence of kaolin in coal on the metabolism of biological methane.