Identifying the role of Cu, Co, or Ni species in exchanged zeolite catalysts by different preparation methods has been widely concerned for selective catalytic reduction by ammonia (NH3-SCR). Here, we found that ammonia wet ion exchange method (AWIE) was useful for increasing ionic species and improving ion polymerization degree in traditional NaY (Si/Al = 2.5) zeolites. Cu, Co, and Ni substituted Y zeolite prepared by AWIE method achieved better SCR performance than those by conventional wet ion exchange method (CWIE). Meanwhile, the coordination states and chemical environments of Cu, Co, and Ni exchanged species influenced the redox and adsorption properties of catalysts. Cu-NH3-IE catalyst had a wider SCR temperature window than Co-NH3-IE and Ni-NH3-IE catalysts owing to its more stable NH3 adsorption, lower temperature, and smaller area of reduction peak. We proposed that the balance of NH3 adsorption and oxidation in thermodynamics and kinetics was the key for high N2 selectivity. This work provided a new idea for modifying the active sites of zeolite catalysts to achieve high activity and N2 selectivity in a broad temperature window.