Mucoepidermoid carcinoma (MEC) is a common malignancy of the salivary glands, which account for approximately 30% of all malignant salivary gland neoplasms that originate in both the major and minor glands. But it is relatively rare at other organs, extremely rare in the hepatobiliary system. To the best of our knowledge, since primary MEC of the liver was first reported in 1971, no more than 20 cases have been reported worldwide. The cellular morphology of MEC can be easily misdiagnosed as adenosquamous carcinoma (ASC). In view of the poor prognosis of MEC, we herein report the morphological, histochemical, immunohistochemical, gene sequencing results and ultrastructural features, which distinguished from ASC through a misdiagnosed case.