Abstract: Objective To investigate the effect of clinical surgical techniques of congenital choledochal cyst on improving liver function and its long-termed effect. Methods We selected 41cases, including 23 males and 18 females, aged 1.5-14 years old, who are suffering from congenital choledochal cyst in Setemper 2009 to December 2013. All the patients were operated on with complete cyst excision combined with Roux-en-Y hepaticojejunostomy after diagnosis by imaging tests. The serum indexes of liver function, total bilirubin (TBil), direct bilirubin (DBil), alanine aminotransferase (ALT), aspartate aminotransferase (AST) before operation were tested to compared with that of one week after operation. Results The result of experiments shows that 27 cases of 41 patients were higher than normal in TBil and DBil, which decreased significantly after the procedure (P ＜ 0.01), the difference means something in statistics. In addition, 14 cases are within the range of normal reference value, their postoperative TBil and DBil shows no significant difference (P ＞ 0.01). Their preoperative ALT and AST indexes were higher than the normal value, which significantly decreased after the operation. There are significant differences between preoperative and postoperative surgery (P ＜ 0.01). Thirty-seven cases which are visited regularly have good prognosis. Two patients suffered from stone formation in bile duct with cholangitis, and their symptoms were relieved after reoperation of lithotomy through original anastomosis, one of them received Partial resection of the left liver with the left lateral lobe of liver fibrosis. Among them there were two case with early postoperative complication, one case acute pancreatitis and the other case of adhesion ileus, both of them were relieved after conservative treatment. Conclusions We draw a conclusion that complete cyst excision combined with Roux-en-Y hepaticojejunostomy is the best surgical method to cure patients suffering from congenital choledochal cyst.