Free radicals, including 1,1-diphenyl-2-picrylhydrazyl, mediate oxidative stress to cause many chronic diseases (including cardiovascular diseases, diabetes and cancer). The extract of traditional Tibetan medicine Lepidium latifolium L. (L. latifolium) was reported to have free radical inhibition ability. Therefore, a system method was established to separate the ethanol extract of L. latifolium to prepare two main antioxidant compounds. First of all, silica gel and a medium-pressure liquid chromatography tower were used for pre-treatment of the ethanol extract of L. latifolium to obtain the main antioxidant active component fraction 4 through online high-performance liquid chromatography-1,1-diphenyl-2-picrylhydrazyl (HPLC-DPPH) assay. Then, fraction 4-1 was obtained by one-dimensional preparation using Megres C18 chromatographic column, and two active compounds with IC₅₀ values 59.9 and 71.3 μg/mL were obtained by two-dimensional preparation using Click XIon chromatographic column. Through the study of the chemical components and separation methods of L. latifolium, the combination of HPLC-DPPH assay and two-dimensional preparative liquid chromatography was realized, providing a reference for the separation of active compounds from L. latifolium.