Abstract: The biliary microbiota is an important component of the biliary system, the structure changes and dysbiosis of the biliary microbiota are closely related to the occurrence and development of biliary diseases. Recent studies have found that the dysbiosis of the biliary microbiota can lead to the occurrence of various biliary diseases such as cholelithiasis, cholangitis, and biliary tract cancer. However, the specific mechanisms of some of these diseases remain unclear. In addition, the alternation of biliary microbiota may also lead to the occurrence of postoperative complications of biliary diseases, such as the risk of infection increased after laparoscopic cholecystectomy (LC) and endoscopic retrograde cholangiopancreatography (ERCP). Although some studies have begun to explore the connection between biliary microbiota and biliary diseases, most research have mainly focused on a single disease type or specific microorganisms. There has been no comprehensive and systematic review of the overall changes in biliary microbiota across different diseases and their association with post biliary surgery infection.Therefore, this article presents a systematic review of current advances linking the alternations of biliary microbiota to the development of biliary diseases and their postoperative infections, as well as the changes in the biliary microbiota before and after various biliary diseases and their surgeries, aiming to provide insightful methods for the early diagnosis, prevention and treatment of biliary diseases and management of postoperative infections.