This study aims to explore the efficacy of interferon-α (IFN-α) combined with either entecavir (ETV) or adefovir (ADV) therapy versus IFN-α mono-therapy for chronic hepatitis B (CHB) patients, and to identify the factors associated with treatment outcomes. Totally, 159 CHB patients receiving interferon-based treatment for 48 weeks were enrolled in this retrospective study, including IFN-α mono-therapy group (group A, n=44), IFN-α plus ADV group (group B, n=53) and IFN-α plus ETV group (group C, n=62). The primary measures of efficacy assessments were the changes in HBsAg. Cox regression analysis was used to identify the predictors of treatment outcomes. The predictive values of the factors were assessed by ROC analysis. For patients with baseline hepatitis B surface antigen (HBsAg) level <1000 IU/mL, the reductions in mean HBsAg levels at week 48 were greater in group C than that in group A (P<0.05). Higher rate of HBeAg seroconversion was achieved in the combined therapy group than in IFN-α mono-therapy group at week 48 (P<0.05). Two factors were independently associated with HBeAg seroconversion: baseline HBeAg level <2.215 log10 index/mL and ΔHBeAg (decline in HBeAg from baseline) >0.175 log10 at week 12. In conclusion, interferon-α plus ETV therapy can accelerate HBsAg decline as compared with interferon-α mono-therapy in CHB patients with lower baseline HBsAg levels, and the combination therapy was superior to IFN-α mono-therapy in increasing the rate of HBeAg seroconversion. Baseline HBeAg and ΔHBeAg at week 12 can independently predict HBeAg seroconversion in patients subject to interferon-based therapy for 48 weeks.