Cholelithiasis is a common and frequently-occurring disease worldwide. Its pathogenesis is a complex process involving both genetic and environmental factors, and has not yet been fully elucidated. The studies of human microbiome discovered that the microecosystem of the gastrointestinal tract participates in maintaining multiple physiological functions, and its imbalance is also related to the pathogenesis of many diseases. Numerous studies on cholelithiasis in recent years suggested that the gastrointestinal tract microecology plays an important role in its pathogenesis. Here, the authors address the relationship between the gastrointestinal tract microecology and cholelithiasis from the perspectives of the role of the gastrointestinal tract microecology in human microecology, the general research situation of the pathogenesis of cholelithiasis, and the relations of biliary microecology and intestinal microecology with cholelithiasis.