To systematically reveal the phenotypic distribution characteristics of soluble sugar content in soybean sprouts from improved soybean varieties in the Huang-Huai-Hai region and to deeply explore its genetic regulatory basis, this study utilized 188 improved soybean varieties from the region. The soluble sugar content in germinated soybean sprouts was accurately measured, and a genome-wide association study (GWAS) was conducted using high-quality SNP markers obtained through whole-genome resequencing. The results showed extensive phenotypic variation in the soluble sugar content of soybean sprouts among the improved varieties from the Huang-Huai-Hai region, with content ranging from 0.17 to 2.09 mg·g?1 and a coefficient of variation of 27.3%. This indicates substantial genetic diversity for this trait within the tested materials. A total of 41,029 high-quality SNP loci were obtained based on resequencing technology. Through GWAS analysis, five SNP loci significantly associated with soluble sugar content (?log??(P) ≥ 5.86) were identified across two years, distributed on chromosomes 2, 10, 12, 14, and 18, respectively. Furthermore, within the intervals of these five associated loci, 18 candidate genes were screened. Their functions are mainly enriched in carbohydrate metabolism pathways, such as gluconeogenesis and trehalose synthesis, as well as pathways related to cell wall synthesis. It was further found that the expression levels of four of these genes differed between materials with high and low soluble sugar content. Their functions were primarily enriched in carbohydrate metabolism pathways such as gluconeogenesis and trehalose synthesis, as well as pathways related to cell wall synthesis. This study clarified the phenotypic variation characteristics of soluble sugar content in soybean sprouts from the Huang-Huai-Hai region and identified key SNP loci and candidate genes regulating this trait. It provides important theoretical support and a practical basis for elucidating the molecular mechanism of soluble sugar synthesis in soybean sprouts, developing functional markers, and conducting marker-assisted breeding.