Seed sugar composition, mainly including fructose, glucose, sucrose, raffinose, and stachyose, is an important indicator of soybean (L.) Merr. seed quality. However, research on soybean sugar composition is limited. To better understand the genetic architecture underlying the sugar composition in soybean seeds, we conducted a genome-wide association study (GWAS) using a population of 323 soybean germplasm accessions which were grown and evaluated under three different environments. A total of 31,245 single-nucleotide polymorphisms (SNPs) with minor allele frequencies (MAFs) ≥ 5% and missing data ≤ 10% were selected and used in the GWAS. The analysis identified 72 quantitative trait loci (QTLs) associated with individual sugars and 14 with total sugar. Ten candidate genes within the 100 Kb flanking regions of the lead SNPs across six chromosomes were significantly associated with sugar contents. According to GO and KEGG classification, eight genes were involved in the sugar metabolism in soybean and showed similar functions in Arabidopsis. The other two, located in known QTL regions associated with sugar composition, may play a role in sugar metabolism in soybean. This study advances our understanding of the genetic basis of soybean sugar composition and facilitates the identification of genes controlling this trait. The identified candidate genes will help improve seed sugar composition in soybean.