Saxifraga atrata is an important traditional Tibetan medicine used to treat cough and pneumonia, and has tremendous medicinal potential. In this study, we devised a technique to separate 1,1‐diphenyl‐2‐picrylhydrazyl inhibitors from a methanol extract of S. atrata. The material was first processed using MCI GEL CHP20P medium‐pressure liquid chromatography, yielding 1.1 g of the target fraction Fr2. Subsequently, online hydrophilic interaction liquid chromatography‐1,1‐diphenyl‐2‐picrylhydrazyl assay was used to identify prospective 1,1‐diphenyl‐2‐picrylhydrazyl inhibitors, and two 1,1‐diphenyl‐2‐picrylhydrazyl inhibitor fractions (Fr24 and Fr25) were identified from Fr2. Then, medium‐pressure preparation was continued using an XIon column to separate two 1,1‐diphenyl‐2‐picrylhydrazyl inhibitor fractions (Fr24 and Fr25). The target compound was concentrated in fractions Fr24 and Fr25 using reverse‐phase liquid chromatography during further separation procedures. Finally, the purity, structure, and 1,1‐diphenyl‐2‐picrylhydrazyl inhibitory activity of the isolated 1,1‐diphenyl‐2‐picrylhydrazyl inhibitors were determined. Two 1,1‐diphenyl‐2‐picrylhydrazyl inhibitors (adenosine with the half maximal inhibitory concentration of 66.87 ± 14.33 μM and (‐)‐4‐O‐(E)‐caffeoyl‐l‐threonic acid with the half maximal inhibitory concentration of 59.06 ± 5.02 μM) were isolated with purities exceeding 95%. The results showed that this technology is effective in the targeted separation of antioxidants from natural products.