Antibiotic resistance genes (ARGs), as emerging environmental contaminants, are becoming a threat to human health. In this study, the combined processes of powdered activated carbon (PAC)/biological PAC (BPAC)–ultrafiltration (UF) were adopted to reduce the levels of ARGs in secondary effluents from a wastewater treatment plant. The removal of dissolved organic carbon (DOC) and the change of normalized flux in the UF process were investigated. In addition, the structural characteristics of the microorganisms of the BPAC were analyzed. The results showed that the appropriate dosage of PAC and BPAC was 40 mg/L. At this dosage, PAC/BPAC–UF combined processes could effectively remove the ARGs in secondary effluents by 1.26–2.69-log and 1.55–2.97-log, respectively; and the removal rates of DOC would be 60.7% and 54.1%, respectively. Relative to the direct UF, the membrane fluxes of the two combined processes were increased by 15.6% and 25.1%, respectively. Significant removal correlations were found between ARGs, intI1, DOC and 16SrDNA. These results revealed that the PAC/BPAC–UF combined process might play a promising role in ARG reduction in secondary effluents from wastewater treatment plants.