Prognosis of hepatocellular carcinoma (HCC) remains unsatisfying due to a lack of early detecting methods. Protein Induced by Vitamin K Absence or Antagonist-II (PIVKA-II) has been proved to be an efficient biomarker for HCC. However, the predicting efficacy of PIVKA-II has barely been reported. In the Hepatitis Biobank of Southwest Hospital (HBS) cohort at Southwest Hospital, we did a two-stage nested case-control study. Totally, 45 HCC cases versus 138 matched controls were enrolled to compare levels of α-fetoprotein (AFP) and PIVKA-II in sequential sera at -12, -9, -6, -3 and 0 months before imaging diagnosis. Levels of both PIVKA-II and AFP in HCC cases elevated significantly at all time points compared with controls. In validation stage, the sensitivity and specificity of PIVKA-II at baseline were 58.3% and 92.6%, and AFP were 75.0% and 91.7%. AFP-/PIVKA-II+ patients covered 27.4%, 29.4% and 19.6% at M-12, M-6 and M-0, respectively, while AFP+/PIVKA-II- patients covered 25.5%, 19.6% and 17.7%, respectively. Both PIVKA-II and AFP have the potential for HCC prediction, while PIVKA-II has a better positive rate than AFP before diagnosis.