The methylation level of the three DMPs (cg13674437/ADAM12: HR (95% CI) = 0.34 (0.14–0.83), cg06758847/PSD3: HR (95% CI) = 4.89 (1.79–13.33), and cg24595678/PSD3: HR (95% CI): 11.19 (3.27–38.35) showed a strong association with HCC progression from cirrhosis regardless HCV infection status at enrollment. Here, PSD3 is linked to hepatocellular carcinoma.