Background: Intrahepatic biliary cystadenoma (IBC) is a rare benign cystic tumor of the liver with carcinogenic potential. Due to its low incidence and lack of specific clinical symptoms and signs, IBC is easily confused with other cystic liver lesions; even today, IBC mistakenly underwent fenestration and drainage according to the hepatic cyst in adverse conditions consequences for patients.Methods: The clinical data of six patients with pathologically defined IBC, admitted to the Department of Hepatobiliary Surgery of the Affiliated Hospital of Guangdong Medical University from January, 2011, to July, 2021 were retrospectively analyzed.Results: Four patients (4/6) were diagnosed with IBC preoperatively, administrated the surgery, and discharged successfully. One patient underwent single-port laparoscopic fenestration and drainage of liver cyst, cyst wall biopsy, intraoperative pathology revealed IBC, then open left hemihepatectomy. Another patient underwent laparoscopic fenestration and drainage of hepatic cyst. Intraoperative pathologic diagnosis from cyst wall biopsy showed a simple hepatic cyst, but the final pathological diagnosis was IBC. The remaining liver volume was insufficient to undergo liver resection; the patient was again referred to our institution after four months with right upper quadrant pain. Computed tomography revealed extensive abdominal nodules, considered malignant transformation, and the patient died three months later.Conclusion: Since atypical IBC is easily misdiagnosed as hepatic cysts, and we propose paying attention to cystic wall morphology and cyst fluid properties during the operation. At the same time, it is recommended that patients diagnosed with liver cysts undergo intraoperative pathological diagnosis and strengthen communication with pathologists to deepen understanding of IBC, which avoids missed diagnosis, wrong operation, or even secondary operation.