As an essential grain, oil, and feed crop worldwide, soybean plays a crucial role. Developing high-yielding and high-quality soybean varieties is a critical goal for breeders. The grain weight per plant and 100-grain weight directly impact the soybean yield. This study combined genotypic data from the population with phenotypic data. Based on genome-wide association analysis (GWAS), GLM and MLM analysis models were used to locate the Gm04_21489088, Gm04_15703616, and Gm04_46466250 are loci related to soybean grain weight per plant, and find the Gm09_20334173, Gm04_39518612 and Gm04_39518624 are loci related to 100-seed weight. After performing a reference comparison, we conducted gene annotation and identified candidate genes Glyma.04G203400 and Glyma.04G125600, potentially associated with grain weight per plant in soybeans. These genes are primarily involved in protein synthesis and cell differentiation processes. The candidate gene Glyma.09G109100, associated with the 100-grain weight trait, was successfully annotated. The analysis revealed that the gene primarily involves enzyme activity, suggesting its potential role in regulating grain weight. These findings offer valuable insights into the mechanism of soybean yield and serve as a critical theoretical foundation and genetic resource for cultivating new soybean germplasm with high yield. These findings are of immense significance for future research endeavors to achieve high-yielding soybean varieties.