The present invention relates to a use of Glycine N-methyltransferase (GNMT) in treating or preventing fatty liver related disease, such as nonalcoholic fatty liver disease (NAFLD) or hepatocellular carcinoma (HCC). The use of GNMT for treating or preventing fatty liver diseases is achieved by enhancing GNMT-NPC2 interaction, and thus decreasing or preventing the accumulation of lipid and cholesterol in hepatic cells or tissues.