The invention discloses a cardamine hupingshanesis water-soluble activated selenium polypeptide extract. The extract is obtained in the following steps that cardamine hupingshanesis is smashed and subjected to water extraction to obtain a water extract, the water extract is filtered by means of a filter screen, residues are removed to obtain filtrate, the filtrate is pressurized and filtered by a filter membrane to obtain microfiltration liquid, the microfiltration liquid is pressurized and filtered by an ultrafiltration membrane with the molecular weight being 1000-3000 Dalton to obtain ultrafiltration liquid, the ultrafiltration liquid is pressurized and filtered by a nanofiltration membrane with the molecular weight being 150 Dalton to remove inorganic salt and water to obtain a nanofiltration concentrated solution, ethyl alcohol is added into the nanofiltration concentrated solution, and the mixture stands still and is filtered to obtain precipitate, namely the cardamine hupingshanesis water-soluble activated selenium polypeptide extract. Large-molecular impurities like pectin, polysaccharide and starch are effectively removed sequentially through microfiltration, ultrafiltration and nanofiltration, and high-purity cardamine hupingshanesis water-soluble activated selenium polypeptide with the molecular weight being 150-3000 Dalton is obtained. The method is a pure physical natural process and is suitable for large-scale production and extraction of cardamine hupingshanesis water-soluble activated selenium polypeptide.