Plant vacuolar Na⁺/H⁺ antiporters play important roles in cellular ion homeostasis,vacuolar pH regulation and sequestration of Na⁺ ions into the vacuole. Previous research showed that hydrophilic C-terminal region of Arabidopsis AtNHX1 negatively regulates the Na⁺/H⁺ transporting activity. In this study, we truncated the hydrophilic C terminus of a vacuolar Na⁺/H⁺ antiporter gene from Salicornia europaea (SeNHX1) to generate its derivative, SeNHX1-𝛥C. Expression of SeNHX1 and SeNHX1-𝛥C in yeast mutant showed that SeNHX1 significantly improved the tolerance to NaCl; however, the expression of SeNHX1-𝛥C enormously decreased the tolerance to NaCl. Overall, these results suggest that the hydrophilic C-terminal region of SeNHX1 is required for Na⁺/H⁺ exchanging activity of SeNHX1.