Bile duct hamartoma in the liver (LBDH) is relatively rare among the hepatic space-occupying lesions that occur in adults, and the malignant transformation of LBDH is even rarer. In the present case report, a 63-year-old male was found to have two space-occupying lesions in the right lobe of the liver upon ultrasound examination. Enhanced computed tomography (CT) suggested benign hepatic haemangioma, and contrast-enhanced ultrasonography (CEUS) suggested well-differentiated hepatocellular carcinoma. The final pathology results revealed the malignant transformation of LBDH into well-differentiated intrahepatic cholangiocarcinoma. Improved recognition of this type of rare disease can be obtained by radiographic analysis of this case. These findings contribute to a better understanding of the enhanced development pattern of this disease on contrast-enhanced CT, as well as on CEUS.