Background. Nucleotide analogues (NTs) monotherapy may have a more significant effect on reducing hepatitis B surface antigen (HBsAg) than nucleoside analogues (NSs) due to their immunomodulatory function. However, this superiority remains unknown when combined with PEGylated interferon α (PegIFNα). Therefore, this study aimed to explore whether NTs have more significant antiviral effects than NSs in combination therapy with PegIFNα. Methods. Chronic hepatitis B (CHB) patients treated with PegIFNα plus nucleos(t)ide analogues (NAs) were retrospectively recruited. Efficacy and the predictors of hepatitis B surface antigen (HBsAg) reduction >1 log10 IU/mL after 48 weeks were analyzed. Results. A total of 95 patients were included and divided into the PegIFNα + NTs group and the PegIFNα + NSs group. Propensity score matching (PSM) was performed. The PegIFNα + NTs group had a greater reduction of HBsAg (−3.52 vs. −2.33 log10 IU/mL,
P
=
0.032
) and a higher proportion of patients with HBsAg reduction >1 log10 IU/mL (100.0% vs. 72.2%,
P
=
0.003
) even after PSM. However, HBsAg and hepatitis B e-antigen (HBeAg) loss rates, HBeAg seroconversion rates, degree of HBeAg and hepatitis B virus (HBV) DNA decline, HBV DNA undetectable rates, and alanine aminotransferase (ALT) normalization rates showed no significant differences. Subgroup analyses showed the difference in the reduction of HBsAg was particularly evident in HBeAg-positive and the “add-on” subgroups. PegIFNα plus NTs (OR = 36.667, 95% CI = 3.837–350.384) was an independent predictor for HBsAg reduction >1 log10 IU/mL after 48 weeks. Conclusion. This study suggests that PegIFNα plus NTs may lead to more HBsAg reduction, especially in HBeAg-positive and “add-on” patients.