Functional dyspepsia is a common refractory disease in clinical settings，and modern medicine has limited efficacy.“Brain-gut-microecology” is a new concept of two-way regulation between the “brain-gut axis” and the intestinal flora，which is closely related to the pathological mechanism of functional dyspepsia.This article summarized the research on the relationship between functional dyspepsia and “brain-gut-microecology”.Meanwhile，based on the characteristics of traditional Chinese medicine in the treatment of functional dyspepsia，such as syndrome differentiation，holistic regulation，small side effects，and long-term use，and the treatment principle of “alleviating physical disease with medicine while emphasizing emotional regulation”，the advantages of traditional Chinese medicine can be made full use in the treatment of functional dyspepsia.This review is expected to serve as a reference basic research and clinical treatment with integrated traditional Chinese and western medicine and the combination of disease and syndrome.