Improving seed composition and quality, including protein, oil, fatty acid, and amino acid contents, is an important goal of soybean farmers and breeders. The aim of this study was to map the quantitative trait loci (QTL) underlying the contents of protein, oil, fatty acids, and amino acids with 1510 single nucleotide polymorphism (SNP) markers using the ‘Hamilton’ × ‘Spencer’ recombinant inbred line population (H × S; n = 93). A total of 13 QTL for the traits studied have been mapped on 3 chromosomes (Chr.) of the soybean genome. Three major QTL have been mapped to a 7–13 cM region on Chr. 6. One major QTL for oil content (qOIL001) explained approximately 76% of the total phenotypic variation in this population; the second major QTL for amino acid alanine (Ala; qALA001) explained approximately 74% of the total variation in Ala content; moreover, two major QTL for palmitic acid (qPAL001 and qPAL002) were identified on Chr. 6 and explained approximately 21% of the phenotypic variation in this population. The SNP markers flanking the QTL identified here will be very useful for soybean breeders to develop and select soybean lines with higher seed composition qualities using marker-assisted selection.