Glycosylation of natural flavonoids with various sugar moieties can affect their physicochemical and pharmacological properties. In this study, the plant flavonoids quercetin aglycon (Quer) and quercetin 3-O-glucoside (Q3G) were evaluated and compared for their potential anti-obesity effects. The Q3G dose-dependently reduced the TG contents and lipid accumulation in 3T3-L1 adipocyte cells, by 52% and 60% at 20μM, respectively, compared to differentiated control (100%), which were 1.6-fold and 2.4-fold higher reduction than Quer. The Q3G (20μM) also more significantly reduced the expression of adipogenic markers such as C/EBP-β, C/EBP-α, PPAR-γ, and aP2 than Quer, indicating that the Q3G suppresses both adipocyte differentiation and lipogenesis more effectively than Quer in vitro. Comparing to those in the high-fat diet (HFD) fed mice control group for 10 weeks, both the body and liver weights and the size of adipocytes in epididymal adipose tissues were significantly reduced in HFD mice fed with Q3G for another 6 weeks (30mg/kg body weight by oral administration), accompanied by the reductions of TG, total cholesterol, and HDL-cholesterol in serum. The Q3G also reduced the levels of the lipid metabolism-associated proteins, PPAR-γ, SREBP-1c, and FAS in the liver tissues. These results clearly demonstrated that Q3G exhibits a stronger anti-obesity effect than Quer and its anti-obesity effect is mediated via inhibition of adipocyte differentiation and lipogenesis, decreasing serum lipid levels by altering hepatic lipid metabolism, and reducing body weight gain. The results of this study suggest that the Q3G, but not Quer, can be a potent functional ingredient of beneficial health foods or a therapeutic agent to prevent or treat obesity.