An isolation method by reversed-phase liquid chromatography coupled with hydrophilic interaction chromatography was successfully used to isolate and purify active bufadienolides from Bufo bufo gargarizans Cantor toad skin. In the first step, crude samples were run on an XTerra Prep C18 column. After screening for activity, two fractions were chosen for further purification. A Click beta-Cyclodextrin (Click-CD) column made in our laboratory was used for the second step. Seven compounds, including four stereoisomers, were obtained at high purity. The orthogonal isolation method described here was a powerful tool for isolating bufadienolides, including stereoisomers, from a natural product. This integrated method may be useful for the discovery of novel active compounds from natural products.