Background: Serum hepatitis B virus RNA (HBV RNA) has been reported to be a surrogate marker of intrahepatic cccDNA during nucleos(t)ide analogs therapy. However, whether HBV RNA is superior to other HBV markers reflecting cccDNA profile in HBeAg-positive patients during peg-interferon (peg-IFN) treatment was still unclear.Methods: Serum HBV RNA, HBcrAg, HBV DNA, and HBsAg were longitudinally assessed among 30 HBeAg-positive patients during 48-week peg-IFN treatment. The intrahepatic cccDNA was detected at baseline and week 48, respectively. The individual correlations between HBV RNA, HBcrAg, HBV DNA, HBsAg, and cccDNA were then statistically analyzed.Results: HBV RNA levels in patients with HBeAg seroconversion decreased more rapidly compared with those without HBeAg seroconversion. Among all patients, cccDNA correlated better with HBV RNA than with HBcrAg, HBV DNA, and HBsAg at baseline. After 48 weeks of treatment, cccDNA still correlated more strongly with HBV RNA than other HBV markers. For subsequent analysis, cccDNA positively correlated with HBV RNA and HBcrAg whereas did not correlate with HBV DNA and HBsAg in patients with HBeAg seroconversion. However, cccDNA highly correlated with HBV RNA and HBV DNA, moderately correlated with HBcrAg, while no correlation was observed between cccDNA and HBsAg in patients without HBeAg seroconversion.Conclusion: Serum HBV RNA correlated more strongly than HBcrAg, HBV DNA, and HBsAg with intrahepatic cccDNA levels before and after 48-week peg-IFN treatment. The level of serum HBV RNA may be a superior surrogate marker reflecting the intrahepatic cccDNA profile in HBeAg-positive patients during peg-IFN treatment.Trial registration: ClinicalTrials, NCT03546530. Registered 1 January 2015. https://clinicaltrials.gov/ct2/results?cond=&term=NCT03546530&cntry=&state=&city=&dist=