Alkali/alkaline earth metals from urea solution and engine lubricating oil can induce the chemical deactivation of NH3-SCR catalysts. Cu-SSZ-39, with excellent catalytic performance and hydrothermal stability, is thought to be a good choice for the NOx abatement from diesel vehicles. In this work, the effects of alkali/alkaline earth metals on Cu-SSZ-39 were investigated for the first time. The deactivation effects of alkali/alkaline earth metals followed the order of K > Mg > Ca > Na. The surface area, isolated Cu²⁺ ions and acid sites greatly decreased after the introduction of alkali/alkaline earth metals. Na and K had greater influence on the zeolite surface acidity than Ca and Mg with the same loading amount (1 mmol per gram catalyst). The deterioration of the zeolite structure and the transformation of isolated Cu²⁺ ions to CuOx were observed after poisoning by each of the alkali/alkaline earth metals. The distribution of copper species is a very important factor determining the SCR performance of Cu-SSZ-39 after alkali/alkaline earth metals poisoning. This work provides a new insight into understanding deactivation mechanisms in Cu-based small-pore zeolites.