A 53-year-old male patient with a previous diagnosis of dilatation of the common bile duct was admitted to the hospital due to recurrent episodes of vague epigastric pain over a 4-month period. After undergoing abdominal CT, MRI, MRCP, ERCP examinations, together with joint diagnosis by the radiology department and the gastroscopy unit, the diagnosis of a cystic dilatation of the common bile duct was excluded, and to preliminarily diagnose as cystic lesion at the hepatoduodenum ligament. A nasobiliary tube was preset before the surgery, and it was found that the gallbladder, the cyst, and the common bile duct were connected in sequence during the surgery, leading to the definitive diagnosis of biliary cyst of the cystic duct. During the surgery, the anatomical position of the common bile duct was accurately identified, avoiding iatrogenic biliary injury and preserving the integrity of the common bile duct structure. The patient recovered and was discharged from the hospital on the 14th postoperative day. Cystic duct cysts are a relatively new and rare condition. This case demonstrates that clinical decision-making by a multidisciplinary team is of great significance for such diseases, and preoperative assessment of the anatomical relationship between cystic dilation lesions in the hepatic portal region and the biliary system and gallbladder is also crucial.