Excessive sodium ion (Na+) concentrations in cultivated land alter crop yield and quality worldwide. Previous studies have shown that shoot Na+ exclusion is essential in most crops for salt tolerance. Here, we show by a genome-wide association study that Zea may L. Na+ content 2 (ZmNC2), encoding the HAK family ion transporter ZmHAK4, confers the natural variation of shoot Na+ exclusion and salt tolerance in maize. The ZmHAK4 locus accounts for ~11% of the shoot Na+ variation, and a natural ZmHAK4-deficient allele displays a decreased ZmHAK4 expression level and an increased shoot Na+ content. ZmHAK4 is preferentially expressed in the root stele and encodes a novel membrane-localized Na+-selective transporter that mediates shoot Na+ exclusion, probably by retrieving Na+ from xylem sap. ZmHAK4 orthologues were identified in other plant species, and the orthologues of ZmHAK4 in rice and wheat show identical expression patterns and ion transport properties, suggesting that ZmHAK4 orthologues mediate an evolutionarily conserved salt-tolerance mechanism. Finally, we show that ZmHAK4 and ZmHKT1 (a HKT1 family Na+-selective transporter) confer distinct roles in promoting shoot Na+ exclusion and salt tolerance, indicating that the combination of the favourable alleles of ZmHKT1 and ZmHAK4 can facilitate the development of salt-tolerant maize varieties.