Cu-SSZ-39 zeolite with an AEI structure exhibits excellent hydrothermal stability and can be a potential alternative to Cu-SSZ-13 zeolite SCR catalysts for NOx removal in diesel vehicles. However, the inferior low-temperature performance of Cu-SSZ-39 leads to substantial NOx emissions during the cold-start period, impeding its practical application. In this study, Ce-Mn oxide-modified Cu-SSZ-39 catalysts (CeMnOx/Cu-SSZ-39) and references (CeO2/Cu-SSZ-39 and MnOx/Cu-SSZ-39) were prepared by the ion-exchange of Cu ions followed by impregnation of the oxide precursors, with the aim of enhancing the NH3-SCR performance at low temperatures. The modified catalysts exhibited improved low-temperature activity and hydrothermal stability compared to the unmodified counterpart. In particular, CeMnOx/Cu-SSZ-39 showed the highest activity among the three catalysts and achieved NOx conversions above 90% within the temperature range of 180 °C to 600 °C, even after undergoing hydrothermal aging at 800 °C. Experimental results indicated that the synergistic effect between Ce and Mn in CeMnOx improves the redox properties and acidity of the catalyst due to the presence of Ce3+, Mn4+, and abundant adsorbed oxygen species, which facilitate low-temperature SCR reactions. Furthermore, the interaction of CeMnOx with Cu-SSZ-39 stabilizes the zeolite framework and hinders the agglomeration of Cu species during the hydrothermal aging process, contributing to its exceptional hydrothermal stability. The kinetics and NO oxidation experiments demonstrated that CeMnOx provides access to fast SCR reaction pathways by oxidizing NO to NO2, resulting in a significant increase in low-temperature activity. This study provides novel guidelines for the design and preparation of Cu-SSZ-39 zeolite with outstanding SCR performance over a wide temperature range.