Abstract: The gut microbiota forms the "microbiota-gut-brain axis" with the gastrointestinal tract and central nervous system, which affects the occurrence and development of central nervous system diseases, such as Alzheimer's disease, Parkinson's disease, depression, and stroke, et al. Natural drugs have shown significant effects and minimal adverse reactions in the prevention and treatment of central nervous system diseases. This article reviews and analyzes research reports on natural drugs based on the "microbiota-gut-brain-axis" to improve central nervous system diseases, summarizes their therapeutic effects and mechanisms of action, in order to provide new ideas for the prevention and treatment of central nervous system diseases and the development of new drugs.