Soybean is rich in nutrients and active substances. Oligosaccharides are beneficial functional components for human health, and identification of soybean oligosaccharide specific germplasms is of great practical significance. In this study, the content of oligosaccharides was quantified by HPLC method in a population of 264 soybean genotypes that were cultivated at multiple environments. The total oligosaccharide content in Sanya city of Hainan province and Nanjing city of Jiangsu Province ranged from 6.18% - 11.46% and 4.19% - 13.80%, respectively. Sixteen oligosaccharide specific genotypes with stable performance at different environments were obtained. Genome-wide association scanning (GWAS) was carried out by combining phenotypic and genotypic data of oligosaccharide content in natural soybean populations. SNPs significantly associated with oligosaccharides content were identified and candidate genes were considered to be related with oligosaccharide/sucrose. Collectively, this study provided germplasm resources applicable for the selection and breeding of special soybean varieties, and also provided foundation for further exploring oligosaccharide candidate genes and developing their molecular markers in soybean.