The amino acids are rich in soybean grains and are important components of the grain quality.In this study， 264 soybean genotypes were analyzed using high-performance liquid chromatography （HPLC） to determine the levels of four free amino acids： arginine， glycine， glutamic acid， and lysine in dried soybean grains. Among the free amino acids， arginine was detected with the highest content， followed by glutamic acid， and glycine. Three soybean varieties with high levels of these four free amino acids were identified， including Haimen Yang 104， Liaoxian Bean 12， and Guanyun Dasiyu. By genome-wide association analysis combined with the phenotypes and genotypes of four free amino acids in soybean natural population， 27 significant SNPs co-located by four amino acids in soybean were identified in two years， among which there were two SNPs for arginine， including S17_19067780 and S17_19067789， and 19 SNPs for glycine，including S01_53974257， S08_38878988，et al， one SNP（S18_53291599） for glutamic acid， five SNPs for lysine，including S08_18555689， S08_18567542， et al. The candidate genes related to high amino acid content in soybean were inferred to be Glyma.17G177400 and Glyma.17G177600 for arginine， and Glyma.11G157000 and Glyma.11G161700 for glycine. Glutamic acid are Glyma.18G244200 and Glyma.18G244700， lysine are Glyma.08G227600 and Glyma.08G228100.The results of this study provide a theoretical basis for improving soybean varieties and assisting soybean molecular breeding.