Cu-exchanged SSZ-16 zeolite catalysts exhibit outstanding NH3-SCR activity, but their catalytic performance after hydrothermal treatments is not ideal. In order to improve the hydrothermal stability of Cu-SSZ-16, CuCex-SSZ-16 series catalysts were prepared via an ion exchange process, and the effect of Ce modification on the hydrothermal stability was investigated. In addition, increasing Ce contents significantly improved the hydrothermal stability, and CuCe0.87-SSZ-16 showed the best hydrothermal stability. The effects of adding Ce to active species and the AFX framework were studied by various characterization measurements. The 27Al MAS NMR results reveal that Ce modification can strengthen the structural stability of the CuCex-SSZ-16 catalysts. Furthermore, the combined results of XPS, H2-TPR, and in situ DRIFTS confirm that the introduction of Ce markedly increases the active Cu2+-2Z species, contributing to the remarkable hydrothermal stability.