In order to study the salt tolerance of Shanxi foxtail millet during germination, to screen candidate genes related to salt tolerance of foxtail millet, and to understand the genetic mechanism of traits related to germination of foxtail millet seeds under salt stress, a total of 333 Shanxi core germplasm was selected for the identification of salt tolerance of foxtail millet during germination. This experiment selected 333 Shanxi core germplasm to study the salt tolerance of Shanxi foxtail millet during the germination stage and to screen for salt-tolerant germplasm materials. A stress of 170 mmol/L NaCl was applied in a light culture room to assess the salt tolerance of the cereals during germination. The subordinate function value method was used to classify the salt tolerance grade of cereals, and the 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 evaluate the salt tolerance of cereals at the germination stage. Combined with the results of core germplasm resequencing, the genome-wide association analysis of salt tolerance at germination stage was carried out. The results showed that the salt tolerance of the core germplasm of the test cereals varied significantly, and the salt tolerance of the 333 core germplasm of the cereals was classified into five categories using the comprehensive evaluation D-value, among which there were 17 high salt-tolerant germplasm. Genome-wide association analysis detected a total of 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, and the analysis screened for the salt tolerance candidate gene Millet_GLEAN_10019153, which was associated with emergence, and haplotyped the gene. The results of this study have certain reference significance for the identification of salt-tolerant cereal germplasm and the mining of salt-tolerant genes.