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Objective: To explore changes and clinical value of serum HBV RNA level on HBeAg positive CHB patients treated with the treatment of Peg IFN-α. Methods: Totally 34 cases of patients with HBeAg positive CHB who received Peg IFN-α treatment in our hospital from February 2014 to October 2015 were selected. Serum HBV RNA, HBV DNA, and ALT levels in patients were detected before treatment, and at treatment of 12 weeks, 24 weeks, and 52 weeks, respectively. The relationship between serum HBV RNA levels and ALT, HBeAg status and response status during Peg IFN-α antiviral treatment was analyzed. Results: The serum ALT level in patients at 12, 24 and 52 weeks after treatment was significantly lower than that in patients before treatment, the serum ALT level in patients at 24 and 52 weeks after treatment was significantly lower than that in patients at 12 weeks after treatment, the serum ALT level in patients at 52 weeks after treatment was significantly lower than that in patients at 24 weeks after treatment, all above had statistical difference (P<0.05). At 12, 24 and 52 weeks after treatment, ALT recurrence rate was 41.18％ (14/34), 55.88％ (19/34), and 76.47％ (26/34), respectively; the negative conversion rate of HBeAg was 26.47％ (9/34), 29.41％ (10/34) and 47.06％ (16/34), respectively; the negative conversion rate of HBV DNA was 38.23％ (13/34), 50.00％ (17/34), and 61.76％ (21/34), respectively. The serum HBV RNA level in patients at 12, 24 and 52 weeks after treatment was significantly lower than that in patients before treatment, all above had statistical difference (P<0.05). At 12, 24 and 52 weeks after treatment, the serum HBV RNA level in patients with recurrent ALT level was significantly lower than that in patients without recurrent ALT level, the serum HBV RNA level in patients with negative conversion of HBeAg was significantly lower than that in patients without negative conversion of HBeAg, the serum HBV RNA level in patients with complete response was significantly lower than that in patients without complete response, all above had statistical difference (P<0.05). The results of Person correlation analysis showed that the serum HBV RNA level was significantly positively correlated with HBV DNA level (r=0.408, P=0.009). Conclusion: During the treatment of Peg IFN-α, the serum HBV RNA level showed an overall downward trend, which was significantly positively correlated with the HBV DNA level. It is expected to serve as an auxiliary indicator for evaluating the efficacy of anti-HBV infection treatment, and has certain clinical value.