With the increasing utilization of nanomaterials, zinc oxide nanoparticles (ZnO NPs) have been reported to induce adverse effects on human health and aquatic organisms. However, the potential impacts of ZnO NPs on wastewater nitrogen and phosphorus removal with an activated sludge process are unknown. In this paper, short-term exposure experiments were conducted to determine whether ZnO NPs caused adverse impacts on biological nitrogen and phosphorus removal in the unacclimated anaerobic-low dissolved oxygen sequencing batch reactor. Compared with the absence of ZnO NPs, the presence of 10 and 50 mg/L of ZnO NPs decreased total nitrogen removal efficiencies from 81.5% to 75.6% and 70.8%, respectively. The corresponding effluent phosphorus concentrations increased from nondetectable to 10.3 and 16.5 mg/L, respectively, which were higher than the influent phosphorus (9.8 mg/L), suggesting that higher concentration of ZnO NPs induced the loss of normal phosphorus removal. It was found that the inhibition of nitrogen and phosphorus removal induced by higher concentrations of ZnO NPs was due to the release of zinc ions from ZnO NPs dissolution and increase of reactive oxygen species (ROS) production, which caused inhibitory effect on polyphosphate-accumulating organisms and decreased nitrate reductase, exopolyphosphatase, and polyphosphate kinase activities.