With the increasingly stringent restrictions on engine exhaust gases, efforts to enhance the activity, hydrothermal stability, and SO2‐tolerance of NH3‐SCR catalysts are highly desirable and challenging. Here, we present the concept of controlled sitings of the metal active sites by modifying Cu‐SSZ‐39 with yttrium (Y) as the rare‐earth metal for enhanced NH3‐SCR performances. Cu(0.25)‐Y(0.12)‐AEI(10) shows superior NOx conversion even after harsh hydrothermal aging at 900 °C, conditions under which standard Cu‐AEI cannot withstand. After long‐term SO2 poisoning, Cu(0.25)‐Y(0.12)‐AEI(10) shows a significantly higher NOx conversion than both Cu‐AEI and conventional Cu‐CHA. The structure‐activity correlation obtained from multiple characterizations, kinetics analyses and DFT calculations reveal that the Y ions act to inhibit dealumination during hydrothermal aging, as a sacrificial agent for SO2‐poisoning, and to stabilize catalytically active Cu centers within the zeolite framework. This synthesis concept provides insight into design of more stable and active NH3‐SCR catalysts in future.