Populus euphratica, the well-known tree halophyte, tolerates the stress of high levels of salt. We previously showed that the transmembrane domain 11 (TM11) of PeNHX3, a Na+,K+/H+ antiporter from P. euphratica, was crucial for Na+ and Li+ transport in a yeast growth assay. Here, we examined the role of TM11 in catalyzing Na+ and Li+ transport in transgenic Arabidopsis. We found that PeNHX3 localized to the tonoplasts in Arabidopsis. Overexpression of PeNHX3 in Arabidopsis improved seedling growth and enhanced salt tolerance and Li+ detoxification. However, overexpression of PeNHX3 did not improve Arabidopsis growth at KCl concentrations higher than 0.1mM, suggesting a low K+ transport activity for PeNHX3 in plants. We performed in planta domain-switch analysis by replacing the C-terminal domain of AtNHX1 with a C-terminal segment of PeNHX3 containing the TM11 domain. We demonstrated that TM11 was critical for the Na+ and Li+ transport activities by PeNHX3. Taken together, PeNHX3 plays an important role in salt tolerance and Li+ detoxification in plants. TM11 controls the Na+ and Li+ transport activities of PeNHX3 in Arabidopsis.