Soybeans are a vital seed crop, supplying a substantial amount of protein and oil globally, for both human and animal consumption. Modern soybean (Glycine max L. Merr.) varieties have been developed through long-term domestication and genetic introgression of wild ancestors (Glycine soja Sieb. and Zucc.). This process involved significant alterations in seed traits, including seed morphology, size, and quality. In recent years, quantitative trait loci (QTLs), and key genes associated with seed domestication traits have been identified via analytical methods such as QTL mapping, genome-wide association studies, whole-genome resequencing, and -omics applications. This review summarizes recent research on domestication-related genes that regulate key seed traits, including size, oil content, and protein content. Additionally, we discuss the application of new technologies, such as -omics technologies, to advance research involving domestication-related genes. This work will help us better understand soybean domestication in terms of seed traits and should expedite the development of elite soybean varieties to meet the growing demands for soybean production, and ensure global food security.