Abstract: At present, there is a lack of high-yield and high-quality soybean varieties in China, so we need to strengthen research and development.Genome wide association analysis（GWAS）has the advantages of high throughput, high precision and less time-consuming.In order to promote the application of GWAS in the process of soybean genetics and breeding, based on the introduction of the theory of GWAS method, this paper summarized its application progress in the genetics and breeding of main agronomic characteristics of soybean, discussed the advantages and disadvantages of GWAS and its development trend, and put forward solutions.