Non-alcoholic fatty liver disease and type 2 diabetes are representing symptoms of metabolic syndrome, which is often accompanied with hepatic fat accumulation and insulin resistance. Since liver is the major site of glucose and lipid metabolism, this study aimed to understand the effects of SCAAs and BCAAs supplementations on glucose and lipid metabolism in HepG2 cells. These cells were pretreated with SAMe, betaine, taurine, and BCAA for 24 h, followed by treatments of a high concentration of glucose (50 mM) or palmitic acid (PA, 0.5 mM) for 48 h to simulate high-glucose and high-fat environments. Pretreatment of BCAA and SCAAs inhibited the fat accumulation. At the transcriptional level, glucose and PA treatment led to significant increase of mRNA gluconeogenic enzyme. The mRNA expression level of GLUT2 was decreased by 20% in the SAMe-treated group and inhibited glucose synthesis by reducing the level of gluconeogenic enzyme. After SAMe or BCAA pretreatment, the mRNA expression of lipogenic enzymes was decreased. The PPAR-γ expression was increased after BCAA pretreatment, but SAMe not only downregulated the expression of PPAR-γ, but also inhibited the expression of ChREBP approximately 20% and SREBP-1c decreased by about 15%. Taken together, the effect of SAMe on glucose and lipid metabolism is significant especially on inhibiting hepatic lipogenesis and gluconeogenesis under the metabolic syndrome environment.