The capacity and mechanism of heterotrophic nitrification-aerobic denitrification (HNAD) strain (H1) to remove carbon, nitrogen, disinfectants chloroxylenol (PCMX) and benzethonium chloride (BEC) were investigated in this study. PCMX was removed via metabolism and chemical oxygen demand co-metabolism process. BEC was eliminated through bacterial adsorption, which greatly inhibited the removal of other pollutants. Carbon source optimization tests revealed that glucose was the optimal carbon source for co-removal of pollutants under mixed disinfectants circumstances (PCMX + BEC). Comparing the groups without (G1) and with disinfectants (G2), the content of extracellular polymeric substances was higher, and hydrophobicity was enhanced under the hazardous conditions of G2. All the nitrogen metabolism functional genes in G2 were up-regulated, and the electron transport system activity was also improved. At the same time, G2 had lower reactive oxygen species content, which reduced the probability of resistance genes dissemination, but the abundance of most quantified resistance genes was elevated in G2. Toxicity assessment assays found a dramatic reduction in the virulence of G2’s effluent compared with the mixed disinfentants. The results confirmed that H1 strain could be used to treat the disinfectant-containing wastewater, which may aid in the application of HNAD process.