In this study, the combined process of slow filtration and low pressure nanofiltration (NF) has been used to deeply remove the antibiotic resistance genes (ARGs) in a secondary effluent, and the mechanism of ARGs removal has been subsequently explored. It is observed that the optimal filtration rate for the slow filtration without biofilm, slow filtration with the aerobic heterotrophic biofilm, slow filtration with the nitrification biofilm and slow filtration with the denitrification biofilm to remove tet A, tet W, sul I, sul II and DOC is 20 cm/h, and the slow filtration with the aerobic heterotrophic biofilm exhibits the highest removal amount. The slow filtration with biofilms removes a high extent of free ARGs. As compared with the direct NF of the secondary effluent and the slow filtration without biofilm-NF, the slow filtration with the aerobic heterotrophic biofilm-NF combined process exhibits the best ARGs removal effect. The microbial population structure and the high filtration rate in the aerobic heterotrophic biofilm promote the removal of ARGs. Strengthening the removal of 16S rDNA, intI 1 and DOC can improve the ARGs removal effect of the combined process. Overall, the slow filtration-NF combined process is a better process for removing ARGs.