The results of multi-omics analyses showed NAFLD was improved by the serine hydroxy methyltransferase 2/glycine/mammalian target of rapamycin/peroxisome proliferator-activated receptor gamma (SHMT2/glycine/mTOR/PPAR-γ) signalling pathway, with the increasing contents of glutathione, total antioxidant capacity, and adiponectin, which may improve oxidative stress, inhibit lipid peroxidation, and reduce the risk of obesity metabolic abnormalities. Here, SHMT2 is linked to obesity due to melanocortin 4 receptor deficiency.