Although the cholesterol-lowering effect of soybean protein has long been widely recognized, little is known about the protein structural characteristics important for its cholesterol-lowering activity. In this process, β-conglycinin (7S) was obviously superior to glycinin (11S). However, the potential ability of 7S protein components to influence obesity and metabolism is still unclear. Therefore, we examined the lipid metabolism ability of 3T3-L1 adipocytes using different 7S subunit deletions to determine their lipid metabolism potential. In this study, we detected the content of cellular triglycerides to evaluate and explore possible potential capabilities. The α-lack group showed low TG accumulation, and the preliminary results show that α-lack had better potential lipid metabolism ability. The difference in protein expression was determined via proteomics analysis. Compared with the HF group, α-lack regulated lipid metabolism through specific mechanisms in the high-fat model, with four pathways significantly up-regulated and 13 pathways down-regulated. It was also found to have the ability to regulate glucose metabolism. The α-lack group could regulate the glucolipid metabolism of 3T3-L1 pre-adipocytes by participating in the oxidative phosphorylation pathway, preventing obesity and diabetes. Finally, in vitro, the accumulation of fats as verified by Oil Red O dyeing is reduced compared with the normal group, and both glucose consumption and glycerol release were significantly reduced (p < 0.01), which further confirmed that α-deficiency played a vital role in lipid metabolism and sugar metabolism. In short, our results indicate that α-lack has potential glycolipid metabolic capacity and is preferable in the preparation of products for human nutritional purposes. These results are also significant for understanding the molecular mechanism of soybean protein in glycolipid metabolism.