Extensive application of carbon quantum dots (CQDs) enlarges its concentration in sewage treatment system. The response of nitrifying sludge to CQDs after long-term exposure was investigated. Results showed that CQD concentrations of 0-100mg/L presented positive effect to enzymes involved in nitrification, accelerating NH4+-N degradation and NO2--N transformation. The oxidation rate of NO2--N was significantly improved from 3.14 to 7.91mg/(L h) under the stress of 100mg/L CQDs. Besides, CQDs stimulated the production of sludge biomass and kept the stability of sludge settleability. Additionally, CQDs were mainly captured by loosely bound extracellular polymeric substances, reducing aromatic-like protein. Microbes alleviated CQD stress by secreting tryptophan-like protein and polysaccharides. After few CQDs entered cells, intracellular antioxidant defense was activated. Total antioxidant capacity level was heightened at least 31%. The activities of superoxide dismutase and catalase were enhanced at relatively low and high CQD concentration levels. Hence, microbial metabolic pathways, microbial community, and nitrifying bacteria were not significantly affected by CQDs. The findings of this work provide new insight for understanding the environmental implication of CQDs in the biological treatment system.