The short-term and long-term effects of Cu nanoparticles (NPs) on partial nitrification (PN) process were studied in SBR. The ammonia oxidation rate, nitrogen removal and sludge property were analyzed within exposure of different concentrations of Cu NPs. The short-term result suggested that the Cu NPs with 1 mg/L was beneficial for PN process, while the NPs in 3-30 mg/L significantly inhibit PN. As a result, the ammonia oxidation rate decreased to 21.9%-44.9% of the initial value. When the Cu NPs was 50 mg/L, the PN process was enhanced, which was mainly because the aggregation reduced the actual concentration of NPs acting on the microorganisms. Long-term exposure within low Cu NPs (1 mg/L) could also suppress the PN process, and the ammonia removal efficiency decreased to 44.8% from 91%. The ammonia-oxidizing bacteria was more severe to the Cu NPs than nitrite-oxidizing bacteria. After the long-term exposure, the copper and extracellular polymeric substance in sludge both increased, and then decreased when no Cu NPs was added to the PN system anymore. Cu NPs performed a significant effect on microbial activity, nitrogen removal ability and sludge property.