Soil salinization has a significant negative impact on the yield and quality of soybean. It is one of the effective ways to improve the yield and quality of soybeans under salt stress by breeding salt-tolerant soybean varieties. ERF transcription factors play an important role in plant response to biotic and abiotic stresses, however, there are few relevant studies in soybean. Based on RNA-Seq data under salt stress, 549 Soybean resequencing data and salt tolerance index data that have been reported in our previous study, as well as the soybean tissue expression data in the Soybean Expression Atlas database, the ERF genes that can respond to salt stress in soybean were identified. Meanwhile, the excellent alleles of ERF genes that can respond to salt stress were identified in 549 soybean resequencing data, and the domestication and artificial selection have also been analyzed. U. The transcriptome data of soybean plants under salt stress showed that 40 of 153 ERF genes were differentially expressed after salt stress, among which 11 genes were up-regulated and 29 genes were down-regulated. Among the 11 up-regulated ERF genes, 8 genes were enriched in roots and distributed on 6 chromosomes. The natural allelic variations of 8 ERF genes that mainly expressed in roots, were identified in 549 natural soybean populations. The results showed that only three ERF genes exist natural variations, among which ERF158H1, ERF166H2, ERF170H1 haplotypes were excellent allelic variations, which could significantly promote salt tolerance of soybean. Nucleotide polymorphism analysis of those excellent alleles showed that ERF170H1 was weakly artificially selected during soybean domestication, while ERF158H1 and ERF166H2 were gradually reduced or lost during domestication process. Therefore, Eight ERF genes that may be involved in the response of soybean to salt stress were identified, and three of them were found to have excellent alleles that can significantly promote soybean salt tolerance. Our findings provide a great significance to enrich and improve the molecular mechanism of soybean response to salt stress and breeding programs for salt-tolerant soybean varieties.