The invention relates to a making method of a high-organic selenium cardamine violifolia selenium polypeptide. The making method comprises the following steps of: S1, performing pretreatment on a rawmaterial: selecting dried cardamine violifolia powder as a raw material for production, performing soaking with ethano for decolorization, performing filtering for removing impurities, and then performing pretreatment with a mixture of cellulolytic enzymes and pectinase to obtain an enzymatic hydrolysate for standby application; S2, performing double-enzyme composite enzymolysis: firstly adding alkaline protease in a supernatant after pretreatment in step S1 for enzymolysis, performing enzyme deactivation, performing cooling to 50 DEG C, adjusting the pH with hydrochloric acid to 6.0-8.0, adding neutral protease, and performing enzymolysis to obtain an enzymatic hydrolysate; and S3, performing enzyme deactivation and peptide solution separation: boiling over the enzymatic hydrolysate to achieve enzyme deactivation, and performing standing to obtain a clear transparent peptide solution in the lower layer. The making method disclosed by the invention has the advantages that the cardamineviolifolia is used a core raw material, and the cellulolytic enzymes and the pectinase are used for pretreatment before enzymolysis, so that the impurities in the cardamine violifolia are effectivelyremoved and the protein extraction rate of the cardamine violifolia is increased; and then a multi-step double-enzyme enzymolysis method is used for enzymolysis, the content of the selenium polypeptide is higher, and the molecular weight of the selenium polypeptide is smaller.