Recent studies revealed that both quantitative hepatitis B surface antigen (qHBsAg) and hepatitis B core-related antigen (qHBcrAg) could serve as a good marker for predicting treatment response and indirectly reflecting intrahepatic cccDNA levels. This study aimed to compare the value of qHBsAg and qHBcrAg in predicting HBeAg seroconversion among patients undergoing PEG-IFN therapy. A total of 31 HBeAg-positive patients, who underwent PEG-IFN therapy for 12 months and follow-up for six months were retrospectively included in this study. The serum qHBsAg level was measured using Elecsys® HBsAg II Quant Assay and serum qHBcrAg level was measured using chemiluminescence enzyme immunoassay. During the 12-month treatment, the absolute levels of serum qHBsAg and qHBcrAg were both lower in patients with HBeAg seroconversion as compared to patients without HBeAg seroconversion, but only the difference in qHBcrAg was significant. During the 6-month follow-up period, both qHBsAg and qHBcrAg levels were rebounded significantly among patients without HBeAg seroconversion. Among patients with HBeAg seroconversion, no sustained significant decline of qHBsAg was observed, but serum qHBcrAg levels continued to decline significantly. The ROC curves analysis showed that both absolute qHBcrAg level and the extent of qHBcrAg decline at month 1 had better performance for the prediction of HBeAg seroconversion at month 6 after treatment, as compared to that of qHBsAg. Early on-treatment qHBcrAg may be a good biomarker for predicting off-treatment HBeAg seroconversion in patients receiving PEG-IFN therapy.