Two kinds of Cu-SAPO-34 catalysts, prepared with a one-pot technique using Cu- tetraethylenepentamine as co-template and an ion-exchange method, were hydrothermally treated at 750 °C for at least 16 h. The migration of Cu species during hydrothermal treatment and the corresponding effect on the selective catalytic reduction (SCR) of NOx were examined and characterized. A certain amount of CuO exists outside and inner the crystallites in the as prepared ion-exchanged sample, whereas copper is mainly atomically dispersed in the one-pot sample existing as isolated Cu2+. After hydrothermal treatment for 16 h, the amount of the inner nanosized CuO in the ion-exchanged sample reduced and the copper disperses to form more isolated Cu2+. However, surface CuO particles increase at the sacrifice of isolated Cu2+ with extending the hydrothermal treatment to 24 h. Aggregation of Cu2+ species also happens during the aging treatment over the one-pot prepared sample where the initial Cu is atomically dispersed as isolated Cu2+. The increase of the amount of the isolated Cu2+ enhances the low-temperature (<350 °C) performance. However, the increase of the amount of surface CuO particles in the aged samples promotes the nonselective NH3 oxidation reaction in the high temperature range and results in the lowering of the SCR activity by limiting NH3 supply.