Soybean (Glycine max) provides vegetable oils and proteins for human consumption. Its production depends on seeds and other production-related agronomic traits. How the seed traits are regulated in soybean remain largely unclear. In this study, we identified a miR172a-ERF416/413 module for regulation of seed traits. The miR172a can cleave the targets ERF416 and ERF413 to affect the downstream gene expression for reduction of soybean seed size and weight. Both the MIR172a-overexpressing transgenic soybean plants and the erf416/413 mutants produce smaller seeds than the control. Consistently, the ERF416-overexpressing transgenic soybean plants generate larger seeds. ERF416 and ERF413 directly targeted to the promotor of GmKIX8-1 and GmSWEET10a to regulate their gene expression for seed size/weight control. Interestingly, the erf416/413 mutants show higher seed yield per plant and higher total seed fatty acid content, whereas the MIR172a-transgenic soybean has lower total seed fatty acid content compared to the control cultivar, suggesting that the miR172a and the ERF416/413 may function in fatty acid accumulation through different pathways. Haplotypes of ERF416 promoter region were further analyzed and Hap1 correlates with higher gene expression and higher seed weight, while Hap3 correlates with higher total seed lipid content. Our study reveals a new module for seed trait control. Manipulation of such alleles should facilitate breeding for high-oil and high-yield soybean cultivars.