Iatrogenic injury in choledocho-pancreatico-duodenal junction is usually difficult to discover in the course of operation because of its unique anatomical position. The injury can lead to postoperative chilis, fever, pain and swelling of the waist, which would easily be misdiagnosed as acute necrotizing pancreatitis. Controlling operations, such as bile and pancreatic juice separation, duodenal diverticularization, jejunal fistulation for enteral nutrition and abdominal drainage should be performed in dealing with the injury in choledocho-pancreatico-duodenal junction. Combined application of pyloric suture with absorbable thread and ligatian, gastric fistulation, ligation of the distal common bile duct and T-tube drainage is minimally invasive, and can fulfill a fully separation of bile and pancreatic juice and duodenal diverticularization. It will improve the possibility of secondary radical operation by ameliorating pyemia and general nutritional condition.