Soybean is an important oilseed crop and major dietary protein resource, yet the molecular processes and regulatory mechanisms involved in biosynthesis of seed storage substances are not fully understood. The B3 domain transcription factor (TF) LEC2 essentially regulates embryo development and seed maturation in other plants, but is not functionally characterized in soybean. Here, we characterize the function of a soybean LEC2 homolog, GmLEC2a, in regulating carbohydrate catabolism, triacylglycerol (TAG) biosynthesis, and seed development. The experimental analysis showed that GmLEC2a complemented Arabidopsis mutant defects in seedling development and TAG accumulation. Over-expression of in Arabidopsis seeds increased the TAG contents by 34% and the composition of long chain fatty acids by 4% relative to the control seeds. Transcriptome analysis showed that ectopic expression of in soybean hairy roots up-regulated several sets of downstream TF genes , Gm that regulate the seed development and production of seed storage substances. regulated the lipid transporter genes and oil body protein gene . The genes involved in carbohydrate biosynthesis and storage, such as sucrose synthesi, and catabolism of TAG, such as lipases in hairy roots were down-regulated. GmLEC2a targeted metabolic genes for seed protein in soybean.