Objective To investigate the clinical effect and safety of balloon-assisted enteroscopy combined with endoscopic retrograde cholangiopancreatography ( ERCP) in patients with altered gastrointestinal anatomy. Methods A total of 12 patients who were admitted to General Hospital of Beijing Military Region from April 2016 to October 2017 and underwent balloon-assisted ERCP after surgical alteration of gastrointestinal anatomy were enrolled, among whom 4 underwent choledochoenterostomy and 8 underwent pancreaticoduodenectomy.Double-balloon enteroscopy was performed for 4 patients and single-balloon enteroscopy was performed for 8 patients. A retrospective analysis was performed for treatment outcome, complications, and prognosis. Results A total of 10 patients underwent balloon-assisted ERCP successfully, resulting in an overall success rate of 83. 3%, and among these patients, 2 had simple anastomotic stenosis and 8 had anastomotic stenosis and intrahepatic bile duct stones. Among the two patients who did not complete ERCP, one had severe anastomotic stenosis which prevented the guide wire from entering the bile duct, and the other patient had a small angle of R-Y intestinal anastomosis which prevented the lens and the cannula from entering the afferent loop. After surgery, one patient experienced jaundice and one experienced perforation of the gastrointestinal tract, resulting in an incidence rate of complications of 16. 7%, and both patients were cured after conservative treatment. Conclusion Balloon-assisted ERCP has good safety and a marked clinical effect with unique complications, as well as a lower success rate than conventional ERCP.