Bile duct injuries can be classified into iatrogenic and non-iatrogenic categories. Non-iatrogenic bile duct injuries include immune, infectious, vascular, ischemic, genetic, idiopathic, and neoplastic causes. After injury, the biliary epithelial cells undergo closely linked pathological processes, such as inflammatory repair, epithelial regeneration, and fibrous repair. These processes interact with inflammatory and stromal cells through autocrine and paracrine mechanisms, coordinating the repair process to maintain the structural and functional integrity of the bile ducts. In the absence of effective intervention, bile duct injuries can lead to bile leakage, biliary strictures, and even progress to cirrhosis, severely affecting the patient's quality of life. Currently, treating bile duct injuries is no longer limited to traditional surgical methods but also includes non-surgical treatments such as immune modulation, bile acid regulation, and gut microbiota adjustment. With the development of medical technology, novel treatments such as gene therapy, stem cell/organoid technology, and endoscopic retrograde cholangiopancreatography/tissue-engineered scaffolds are gaining attention and are expected to become effective treatment options for bile duct injuries in the future. This review focuses on the etiology and pathological mechanisms during the repair process of bile duct injuries and summarizes existing and potential treatment approaches, providing a reference for future research and clinical management of bile duct injuries.