Seed weight is an important botanical and evolutionary characteristic in wild soybean. The study objective was to illustrate phenotypic variation in relation to seed weight. A total of 6169 wild soybean accessions were divided into seven types by 100-seed weight and phenotypic traits in each type were evaluated. The results indicated that the smallest seed size type had the lowest average seed oil content (9.04%), which rose gradually to the highest value of 17.81% in the largest seed size type. The two smallest-seeded size types showed the highest values in average protein content (in seeds) and maturity time, respectively, and there seemed to be declines in the two quantitative traits with increasing seed weight. In qualitative traits, there were also trend changes from small to large seed size types. Furthermore, the medium seed size type had the highest genetic diversity (H = 1.136), which decreased as seeds became smaller or larger. These results revealed the evolutionary changes of phenotypic traits as seeds became larger in size. Finally, the findings that large-seeded types were disproportionately distributed in the main soybean-producing area lend weight to the suggestions that some accessions with large seeds might originate from the natural hybridization between wild and cultivated soybean.