Microbiota-gut-brain axis （MGBA） plays a role of bidirectional regulation between gut microbiota and brain， and the change in intestinal environment， especially gut microbiota， can act on the central nervous system of human and thus lead to psychological and behavioral changes such as anxiety and depression， which in turn affects gastrointestinal motility and digestion-absorption function. At present， more and more studies have shown that MGBA plays an important role in functional gastrointestinal diseases， and the pathways involved included the neural signaling pathway， immune response， endocrine and role of metabolites. This article reviews the theoretical basis for the formation of MGBA and summarizes the studies on its application in functional gastrointestinal diseases， in order to provide new ideas and methods for the research and clinical treatment of functional gastrointestinal diseases.