In order to investigate the salt tolerance of Shanxi foxtail millet during germination， identify candidate genes associated with this trait， and elucidate the genetic mechanisms underlying germination traits under salt stress， a total of 333 core germplasms from Shanxi， China， were selected for assessing salt tolerance during germination. A stress of 170 mmol/L NaCl stress treatment was applied in a controlled light chamber to determine the salt tolerance during germination. The subordinate function value method was used to categorize the salt tolerance grades of the millets， and a comprehensive evaluation D value of five related traits， namely， relative germination potential， relative germination rate， relative root length， relative shoot length， and relative germination index， was used to access salt tolerance at the germination stage. In conjugation with the resequencing results of core germplasm， a genome-wide association scanning （GWAS） for salt tolerance at the germination stage was carried out. The findings revealed significant variation in salt tolerance in the collection， which were classified into five categories using the comprehensive evaluation D-value， with 17 exhibiting high salt tolerance. GWAS identified 84 single nucleotide polymorphism （SNP） loci associated with salt tolerance during emergence. Functional annotation was performed on the genes where the significantly associated SNPs were located. This led to the identification of the salt tolerance candidate gene Millet_GLEAN_10019153， which is associated with emergence. The outcomes of this study offer valuable references for the identification of salt-tolerant cereal germplasm and the mining of salt-tolerant genes.