Abstract: 【 Objective 】So in view of this, our project aims to explore excellent salt tolerant soybean germplasm resources and identify stable expression sites related to salt tolerance.【 Methods 】In this study, 250 mmol/L NaCl solution was used to simulate the saline-stressed growth environment, and treat 301 soybean seedlings. 7 days later,five traits including total number of roots, number of root tips, total length of roots, root fresh weight,root dry weight were measured and then salt tolerance of soybean seedling was evaluated by principal component analysis(PCA), membership function analysis, and cluster analysis based on stress indices of various indicators, and finally, genome-wide association analysis(GWAS)was conducted based the root trait value under different treatment conditions.【 Results 】According to the strength of salt tolerance, the 301 materials could be divided into 4 categories. 4 strong salt tolerant varieties were classified as the first category, 73 salt tolerant varieties classified as the second category, 137 moderate salt tolerant varieties classified as the third category, and 87 salt sensitive varieties classified as the fourth category. GWAS showed that under normal treatment, two significant SNP loci were detected in root fresh weight, total root length, and total root number. A total of 7 SNP loci that might be associated with salt tolerance traits in soybean roots were detected under salt stress conditions, including the total number of roots and the number of root tips.【 Conclusion 】The phenotype of soybean root system is closely related to soybean salt tolerance, and screening sites related to salt tolerance through GWAS provides effective basis for the cultivation of new salt tolerant soybean varieties. A total of 9 significant SNP loci possibly related to salt tolerance traits in soybean roots were detected.