The continuously updated after-treatment system of diesel engines drives the selective catalytic reduction of ammonia (NH 3 -SCR) catalysts to withstand hydrothermal stability at higher temperatures (>800 °C). To meet the tightened emission of nitrogen oxides (NO x ), yttrium ions (Y 3+ ) were employed to improve the hydrothermal stability of the Cu/SSZ-39 catalyst at 900 °C. X-ray diffraction, solid nuclear magnetic resonance, H 2 temperature-programmed reduction, NH 3 temperature-programmed desorption, and in situ diffuse reflectance infrared Fourier transform spectra verified the key role of Y 3+ on the stability of the structure of SSZ-39 zeolite and the isolated copper species. In detail, the optimized structural stability at 900 °C of the Y-modified Cu/SSZ-39 catalyst is achieved as a result of the spatial and electronic effects of Y 3+ at ion-exchanged sites. Furthermore, Y 3+ ions in the cages of SSZ-39 zeolite induce more isolated copper species in the double six-member rings of SSZ-39 zeolite. The modified catalyst by 1 wt % Y (Cu/Y 1.0 -SSZ-39) shows the best deNO x performance after hydrothermal aging at 900 °C for 10 h, including higher than 70% NO x conversion at 200−550 °C and the maximum NO x conversion of 94% at 300 °C, which is remarkably higher than the maximum NO x conversion of 38% over Cu/SSZ-39 after same hydrothermal aging. This work provides a vital research strategy for fabricating the extraordinary hydrothermally stabilized Cu-based zeolite catalysts for NH 3 -SCR reaction, which would meet the "near-zero" emission after hydrothermal aging at 900 °C in the future.