In this study, a novel process for swine wastewater treatment, anoxic and four-stage micro oxygen aerated sequence coupled with a coagulation process (AO(4)) was investigated in the pilot scale to determine its capacity in the removal of antibiotics and antibiotic resistance genes (ARGs). Results showed that long-term low dissolved oxygen (DO) operational condition played a significant role in decreasing the antibiotics and relative abundance of ARGs. Around 98% of the total antibiotics were removed along with 4-6 orders magnitude reductions of the ARGs copy numbers in AO(4) process. Reduction of bacterial endogenous decay rate in AO(4) process with low DO (0.15 mg/L and 0.10 mg/L) might result in the increase in the total bacterial population size and the concentration of sludge. As a result, high biomass accelerated the accumulation of antibiotics in sludge. In addition, real-time polymerase chain reaction amplification (qPCR) assays indicated that the long-term low DO could reduce the relative abundance of ARGs via enriching the 16S rDNA in activated sludge and inhibiting the emergence or distribution of ARGs. Our findings imply that the AO(4) process could not only achieve a significant reduction of conventional contaminants such as chemical oxygen demand (COD), chemical oxygen demand (COD), total nitrogen (TN) and total phosphorus (TP) but also antibiotics and ARGs.