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， including sucrose， raffinose， stachyose and total oligosaccharide， were quantified by high performance liquid chromatography （HPLC） method in a population of 264 soybean genotypes that were cultivated at two environments. It was shown that among the three oligosaccharides， sucrose accounts for the highest proportion of total oligosaccharides， and raffinose accounts for the lowest proportion. 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. Ten oligosaccharide specific genotypes with stable performance at different environments were obtained. Genome-wide association study（GWAS） was carried out by combining phenotypic and genotypic data of oligosaccharide content in natural soybean population. 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.