As one of the most urgent social and health problems in the world, neurological diseases have always been attracted by researchers. However, the pathological mechanisms and therapeutic approach are not achieved. In addition to the established roles of oxidative stress, inflammation and immune response, the changes of gut microbiota are also closely related to the development of neurological diseases. Emerging insights on the roles of gut microbiota have confirmed its indispensability in the development of neurological diseases, including neurodegenerative diseases and neuropsychiatric diseases. The dynamic bidirectional communication pathway between gut microbiota and central nervous system is called “gut-brain axis”, which involves immune, metabolic and neural pathways. In this review, we discussed the complex relationship between gut microbiota and the central nervous system from the perspective of gut-brain axis, reviewed the mechanism of microbiota in different neurological diseases, and prospected the employment of gut microbiota in the therapeutic approach of those diseases.