To further improve the activity of Selective Catalytic Reduction of nitrogen oxide (NOx) with Ammonia (NH3-SCR) and the hydrothermal stability at 900 °C on Cu-based small-pore zeolite catalyst, the interaction between ammonia water and Cu2+ is used to regulate the interaction between Cu2+ and Si-O-Al structures of the zeolite, and affect the migration of Cu2+ in the channels of zeolite. The characterization results show that the microchemical environment of isolated Cu2+ species is optimized, and more isolated Cu2+ species can stably exist over the surface of Cu/SSZ-39, exhibiting a strong redox property. Besides, the ability of acid sites to adsorb and activate NH3 is also enhanced, and the amount of H2O adsorbed in the pores of zeolite is reduced due to the stable surface isolated Cu2+ species, which is conducive to the stability of the catalyst after hydrothermal aging at 900 °C. When the mole ratio of ammonia and copper is 3, the NH3-SCR performance and the hydrothermal stability at 900 ºC are both optimized on the modified catalyst. The temperature window that the NOx conversion is higher than 90% (ΔT90) on the unmodified catalyst is 200–475 °C, but the ΔT90 on the modified catalyst is broadened to 178–544 °C. More importantly, after hydrothermal aging at 900 ºC, the ΔT90 on the modified catalyst is shifted to the higher temperature by 48 ºC, with the maximum NOx conversion of 96%. This work would provide a new strategy for further optimizing Cu/SSZ-39 catalyst for deNOx emitted from diesel engines to meet higher emission standards in future.