For hypomethylated up-regulated oncogenes, our results showed that HCC patients with higher methylated expression of CDC5L-cg05671347 (HR = 0.561, 95% CI: 0.328–959, P=0.035), RHOA-cg05657651 (HR = 0.567, 95% CI: 0.402–0.801, P=0.0013), and YBX1-cg16304148 (HR = 0.518, 95% CI: 0.364–739, P=0.00028) had higher OS. Here, RHOA is linked to hepatocellular carcinoma.