Laparoscopic cholecystectomy (LC) has gradually become the first choice for the treatment of cholecystolithiasis in recent years. Iatrogenic bile duct injury (IBDI) is an important clinical problem in LC. The anatomical variation of the cystic duct increases the probability of IBDI and the difficulty of operation. We present a case of a 44-year-old male with a anatomical variation of the cystic duct complicated with cholecystolithiasis and choledocholithiasis, who successfully underwent choledocholithotomy, choledochoscopic exploration and T-tube drainage surgery. The patient recovered well and was discharged home on postoperative day 10. The T-tube was removed at 1 month postoperatively after cholangiography examination of no choledocholithiasis left.