Wastewater treatment plants (WWTPs) have shown to be effective in reducing the abundance of antibiotic resistance genes (ARGs), serving as a crucial barrier to the transmission of ARGs through wastewater. However, the risk of those ARGs remaining in the effluent requires further investigation. In this study, influent and effluent samples from WWTPs with different process configurations were collected for metagenomic sequencing. A total of 1331 ARG subtypes were detected in influent, with total abundance ranged from 0.46 to 3.89 copies/cell, which was higher than global level. The total abundance of ARGs was effectively reduced in effluent with removal efficiency 63.2–94.2%, resulting in a relatively low level when compared with other cities worldwide. Despite the effectiveness in reducing the abundance of ARGs, 4.38% ARGs remaining in effluent were identified as Rank I by arg_ranker with APH(3”)-Ib, ere(A), and sul1 as the most abundant subtypes. Further, metagenomic assembly showed that these high-risky ARGs co-occurred with mobile genetic elements (transposase, recombinase, relaxase, and integrase) and were primarily carried by WHO priority pathogens (Salmonella enterica and Pseudomonas aeruginosa), indicating their high-risky potentials. Taken together, these results indicated that even though WWTPs effectively reduced the abundance of ARGs, the potential risks of remaining ARGs still cannot be neglected. These results might be helpful for controlling the spread of ARGs from WWTPs into neighboring ecosystems.