Background: The liver cyst is a common disease in hepatobiliary surgery. Most patients have no apparent symptoms and are usually diagnosed accidentally during imaging examinations. The vast majority of patients with liver cysts follow a benign course, with very few serious complications and rare reports of malignant changes. Case Presentation: We present two cases of liver cysts that evolved into intrahepatic tumors during the follow-up process. The first patient had undergone a fenestration and drainage operation for the liver cyst, and the cancer was found at the cyst’s position in the third year after the procedure. Microscopically, bile duct cells formed the cyst wall. Tumor cells can be seen on the cyst wall and its surroundings to form adenoid structures of different sizes, shapes, and irregular arrangements, some of which are arranged in clusters. The second patient was regularly rechecked after discovering liver cysts, and a new mass appeared very close to the cyst. The clinical manifestations and laboratory examinations of the two patients lacked specificity, the preoperative diagnosis was unclear, and the postoperative pathology confirmed cholangiocarcinoma.Conclusions: Our cases indicate that liver cysts may lead to the occurrence of malignant intrahepatic cholangiocarcinoma. Therefore, follow-up of particular liver cysts is necessary, and the differential diagnosis of the intrahepatic cystic tumors needs to include cholangiocarcinoma.