The increasing use of cupric oxide nanoparticles (CuO NPs) has raised concerns about their potential environmental toxicity. Aerobic granular sludge (AGS) is a special form of microbial aggregates. In this study, the removal efficiencies of nitrogen and phosphorus, enzyme activities and microbial community of AGS under long-term exposure to CuO NPs (at concentrations of 5, 20, 50 mg/L) in aerobic/oxic/anoxic (A/O/A) sequencing batch reactors (SBRs) were investigated. The results showed the chronic toxicity caused by different concentrations of CuO NPs (5, 20, 50 mg/L) resulted in increases in the production of ROS of 110.37%, 178.64%, and 188.93% and in the release of lactate dehydrogenase (LDH) of 108.33%, 297.05%, 335.94%, respectively, compared to the control. Besides, CuO NPs decreased the activities of polyphosphate kinase (PPK) and exophosphatase (PPX), leading to lower phosphorus removal efficiency. However, the NH4+-N removal rates remained stable, and the removal efficiencies of TN increased due to the synthesis of nitrite and nitrous oxide (N2O) reductases. In addition, CuO NPs at concentrations of 0, 5, 20 mg/L increased the secretion of protein (PN) to 90, 91, 105 mg/gVSS, respectively, which could alleviate the toxicity of CuO NPs. High-throughput sequencing showed that CuO NPs increased the abundance of nitrogen-removal bacteria and reduced the abundance of phosphorus-removal bacteria, which is consistent with the results of pollutant removal upon long-term exposure to CuO NPs.