The effect of Cu(II) shock loads on shortcut biological nitrogen removal during a continuous-flow anoxic/aerobic process was investigated using a hybrid biofilm nitrogen removal reactor. The results demonstrated that [Formula: see text]-N removal was not affected by any Cu(II) shock loads, but TN removal was inhibited by Cu(II) of shock loads of 2 and 5 mg/L, and the performance could not be recovered at 5 mg/L. Furthermore, the TN removal pathway also changed in response to Cu(II) concentrations of 2 and 5 mg/L. Denitrification is more sensitive to Cu(II) shock in SBNR processes. Examination of amoA communities using quantitative PCR showed that the abundance of AOB in the aerobic tank decreased after Cu(II) shock with 5 mg/L, which supported the observed changes in [Formula: see text]-N removal efficiency. The abundance of denitrification genes declined obviously at Cu(II) concentrations of 2 and 5 mg/L, which explained the decreased TN removal efficiency at those concentrations.