Biliopancreatic diseases share common embryonic origins, close anatomical relationships, interconnected physiological functions, and similar disease spectra, with substantial similarities in their pathogenesis, clinical manifestations, diagnosis, and treatment. Therefore, an integrated perspective is important for identifying the underlying causes, standardizing clinical management, and optimizing therapeutic strategies for biliopancreatic diseases. However, current clinical practice is still characterized by excessive subspecialization and fragmentation, insufficient holistic thinking, overreliance on imaging findings with inadequate attention to pathological evidence, and insufficient recognition of the function and preservation of the sphincter of Oddi. For challenging conditions, including unexplained biliopancreatic duct dilatation, pancreatic-segment choledochal cysts, distal bile duct strictures, and sphincter of Oddi dysfunction, comprehensive assessment of the biliopancreatic system should be emphasized. Multidisciplinary team management and systematic follow-up should be incorporated into clinical decision-making to reduce missed diagnoses, inappropriate treatment, and overtreatment. Meanwhile, research from an integrated perspective should focus on the patterns of biliopancreatic duct confluence, the pathogenesis and precision management of biliopancreatic malignancies, and the basic and clinical characteristics of sphincter of Oddi function, thereby further improving the scientific, standardized, and effective management of biliopancreatic diseases.