CAX3 is a vacuolar proton/cation exchanger. To examine the role of CAX3 in salt stress, transgenic Arabidopsis over-expressing AtCAX3 or NtCAX3 was challenged with NaCl. CAX3-expressing Arabidopsis (CAX3-Arabidopsis) exhibited higher salt tolerance, lower accumulation of Na+, and increased Ca2+ level compared with the control plants. In support of this, CAX3-Arabidopsis exhibited less uptake and a higher export rate of Na+, as well as greater uptake and reduced export rate of Ca2+. Regarding the lower Na + level, the expression of HKT1 (Na+ uptake from the xylem) was reduced, whereas that of SOS1 (Na+ exporter) was enhanced. Furthermore, the expression of CNGC10 (Ca2+ importer) was higher, whereas that of ACA8 and ACA10 (Ca2+ exporters) was lower in CAX3-Arabidopsis compared with control plants. Transgenic Arabidopsis exhibited less oxidative stress (superoxide, hydrogen peroxide, and malondialdehyde) but greater activity of antioxidant enzymes (catalase, glutathione reductase, and superoxide dismutase), in accordance with higher salt tolerance. Additionally, atcax3 knockout Arabidopsis exhibited opposite phenotypes compared with CAX3-expressing plants, including lower salt tolerance with increased Na+ level, lower Ca2+ content, and reduced SOS1 expression. CAX3-Arabidopsis exhibited higher abscisic acid level and stomatal closure. Together, these findings indicate that CAX3 enhances salt tolerance by reducing Na+ accumulation, reactive oxygen species, and stomatal opening by increasing Ca2+ levels in Arabidopsis.