Obesity, a major health problem worldwide, is a complex multifactorial chronic disease that increases the risk for insulin resistance, type 2 diabetes, coronary heart disease, and hypertension. In this study, we assessed methods to isolate hypaphorine, a potent drug candidate for obesity and insulin resistance. Semi-preparative reversed-phase liquid chromatography (semi-preparative RPLC) was established as a method to separate three compounds, adenosine, l-tryptophan, and hypaphorine, from the crude extracts of Caragana korshinskii Kom. Due to its specific chemical structure, the effect of hypaphorine on differentiation and dexamethasone (DXM) induced insulin resistance of 3T3-L1 cells was investigated. The structures of the three compounds were confirmed by UV, H-NMR, and C-NMR analysis and compared with published data. The activity results indicated that hypaphorine prevented the differentiation of 3T3-L1 preadipocytes into adipocytes by down-regulating hormone-stimulated protein expression of peroxisome proliferator activated receptor γ (PPARγ) and CCAAT/enhancer binding protein (C/EBPα), and their downstream targets, sterol regulatory element binding protein 1 c (SREBP1c) and fatty acid synthase (FAS). Hypaphorine also alleviated DXM-induced insulin resistance in differentiated 3T3-L1 adipocytes via increasing the phosphorylation level of Akt2, a key protein in the insulin signaling pathway. Taken together, we suggest that the method can be applied to large-scale extraction and large-quantity preparation of hypaphorine for treatment of obesity and insulin resistance.