The growth and development of the central nervous system is influenced by both intrinsic and extrinsic factors. Over the past decade, it has been shown that the activity of microorganisms residing in the gut (microbiome) has direct and indirect effects on the structure and function of the central nervous system. Metabolites produced by gut microbes may cross the intestinal barrier and enter the circulatory system, and by crossing the blood-brain barrier, reach the central nervous system and affect its functions. The gut microbiome can also increase the secretion of bioactive substances by intestinal epithelial endocrine cells. Microbial compounds such as lipopolysaccharide and other metabolites produced by the microbiota can activate the immune system and directly affect the central nervous system through the release of cytokines. Gut bacteria influence the growth, development, and function of the central nervous system by regulating neurogenesis, myelination, modulating glial cell function, synaptic plasticity, and blood-brain barrier permeability, and are implicated in various disorders. Central nervous system disorders such as depression, anxiety, and Alzheimer's disease affect the quality of life of patients and pose a significant economic and social burden worldwide. Due to their obscure and complex pathogenesis, current treatments for these diseases have limited efficacy. In addition to direct interactions between the gut microbiota and the central nervous system, the gut microbiota and their metabolites can regulate epigenetic processes, including DNA methylation, histone modifications, and non-coding RNAs. This review discusses the tripartite relationship between the gut microbiota, epigenetic processes, and central nervous system disorders. According to the information provided, it can be seen that gut microbes and their metabolites influence the pathogenesis of central nervous system disorders at the epigenetic level. This could help in the development of effective therapeutic strategies for central nervous system disorders.