Soybean seed hardness is an important quality character in soybean food processing. Both vegetable soybean and natto require soft seeds to achieve a desirable sensory experience and for effective processing. In this study, we used a texture analyzer to measure the seed hardness of Chinese mini core collection via two indexes over 4 years and found significant correlations among the seed hardness, seed oil content, and germplasm eco-region. Based on 1514 SNPs, genome-wide association studies (GWAS) were conducted using a mixed linear model (MLM). Seventeen SNPs were identified to be associated with seed hardness in at least two environments. Among them, one locus, designated Q-15-0087770, was associated with two indexes, and 13 putative genes were confirmed based on their annotations in SoyBase. This research provides new insights into advanced marker-assisted selections for breeding soybeans for seed hardness and oil content. [ABSTRACT FROM AUTHOR]