Objective To explore surgery strategy of reoperation for type Ⅳa congenital choledochal cyst. Methods The patient was a 20-year-old female with repeated right upper abdominal pain and fever for more than 1 year and aggravation for more than 1 month, and the choledochal cyst excison was performed 15 years ago. The MRI revealed that a huge cyst located in the left lobe of liver, with multiple intrahepatic calculus. The patient was diagnosed with a type Ⅳa congenital choledochal cyst and choledochojejunostomy later and the intrahepatic dilated bile duct was untreated. Results The cystic dilatation of the intrahepatic bile duct was confirmed during the reoperation, and the multiple stones with pus formation were seen, the color of the right liver was normal and the anatomical left hemihepatectomy was performed. The original anastomosis had no stenosis then was preserved. An about 1.5 cm length of extrahepatic bile duct was dissociated from the upper of anastomosis, and the extrahepatic bile duct was cut open and explored with a choledochoscope. The T-tube drainage was performed following removing the stone. The patient recovered well and was discharged smoothly following the surgery. The cholangiography 6 weeks later revealed that the biliary tract was patency and there was no residual stone. There was no jaundice or fever afterwards. Conclusion Complete excision of choledochal cyst and hepaticoduodenostomy is widely accepted as a standard surgery for type Ⅳa congenital choledochal cyst.