Salt stress is a major environmental factor adversely affects crop growth and yield. Wheat as an important food crop has abundant germplasm resources, and the natural variation accumulated in the long-term natural evolution and artificial selection is the basis of many important traits. Therefore, Identification and utilization of excellent allelic variation of salt stress response genes is one of the important ways to improve salt tolerance in wheat. Here, we identified variations in the high affinity K+ transporter gene TaHKT9-7B using genome-wide association mapping (GWAS) with 430 wheat accessions collected from different regions. The results of association analysis between genetic variation and salt tolerance phenotype at seedling stage showed that a 8-bp insertion/deletion (InDel) in the promoter of TaHKT9-7B significantly affects the salt tolerance of wheat. Notably, we identified an ARF recognition site (TGTCGG) located within a 8-bp insertion variant of InDel-1077, and TaHKT9-7B regulates salt stress responses in wheat through differences in expression levels regulated by TaARFs, which targets In-1077 variant to transcriptionally activate TaHKT-7B. We propose that natural variation in TaHKT9-7B promoter affects wheat salt tolerance, and over expression of TaHKT9-7B in Arabidopsis and wheat increased salt sensitivity of plant compared to wild type. In summary, our findings increase the understanding of the mechanisms underlying TaHKT9-7B-mediated salt-stress responses in wheat.