The genes of sulfur-containing amino acid synthetases in soybean are essential for the synthesis of sulfur-containing amino acids. Gene mining of these enzymes is the basis for the molecular assistant breeding of high sulfur-containing amino acids in soybean. In this study, using software BioMercator2.1, 113 genes of sulfur-containing amino acid enzymes and 33 QTLs controlling the sulfur-containing amino acids content were mapped onto Consensus Map 4.0, which was integrated by genetic and physical maps of soybean. Sixteen candidate genes associated to the synthesis of sulfur-containing amino acids were screened based on the synteny between gene loci and QTLs, and the effect values of QTLs. Through a bioinformatic analysis of the copy number, SNP information, and expression profile of candidate genes, 12 related enzyme genes were identified and mapped on 8 linkage groups, such as D1a, M, A2, K, and G. The genes corresponding to QTL regions can explain 6%?38.5% genetic variation of sulfur-containing amino acids, and among them, the indirect effect values of 9 genes were more than 10%. These 12 genes were involved in sulfur-containing amino acid metabolism and were highly expressed in the cotyledons and flowers, showing an abundance of SNPs. These genes can be used as candidate genes for the development of functional markers, and it will lay a foundation for molecular design breeding in soybean.