Key message <p>Six candidate genes for salt tolerance were identified through a accumulation of QTL mapping, GWAS, and transcriptome analysis. Additionally, the accumulation of favorable alleles significantly improved salt tolerance.</p> Abstract <p>Salinization in China is primarily concentrated in the northeast, northwest, and north regions, which overlap heavily with maize-growing areas, severely affecting maize production. Therefore, it is essential to uncover the genetic basis of salt tolerance and enhance maize’s salt tolerance. In this study, we evaluated the survival rates of a BC₂F₇ population and a natural population under salt stress across three environments, revealing significant variation among the accessions. We then performed quantitative trait loci (QTL) mapping and genome-wide association study (GWAS) using genotyping data from 11,312 single nucleotide polymorphisms (SNPs) in the BC₂F₇ and 3,619,762 SNPs in the natural population. As a result, we identified three QTLs and 187 significant SNPs, including one QTL and 19 SNPs consistently detected across multiple environments. To identify candidate genes, we integrated QTL mapping, GWAS results, and dynamic transcriptome analysis under salt treatment. Six candidate genes were identified as potential contributors to salt tolerance. Furthermore, though the favorable alleles of the candidate genes can improve the salt tolerance in maize, there are relatively few germplasm in the natural population that simultaneously possess multiple favorable alleles. In the future, molecular marker-assisted selection could be employed to introgress these favorable alleles into elite lines to enhance their salt tolerance. This study has expanded the understanding of the genetic basis underlying salt tolerance in maize at the seedling stage, providing critical molecular targets for salt tolerance in maize, which facilitates yield increase in saline-alkali soils.</p>