The culture medium in biogas field have been used in coalbed gas bioengineering (CBGB). However, there is a huge difference between the substrate of biogas fermentation and coal. It is necessary to study and optimize the culture medium in the anaerobic digestion (AD) system with coal as substrate. In this study, the single factor test and response surface curve analysis are used to clarify the essential components in the culture medium and the optimal content of these chemicals. The influence of a single component on microbial community structure and major metabolic pathways in AD system are discussed. Under the optimal conditions, SEM observation show that the coal surface sediment is significantly reduced after AD process. The results of GC-MS show that there is no significant difference in the composition and content of organic compounds in the liquid phase before and after the optimization; the microbial community structure and gene function did not weaken with the decrease of culture medium addition, but formed a more targeted and stable microbial community.