The invention relates to a construction method and application for a food-borne polypeptide antioxidant activity three-dimensional quantitative structure-activity relationship model. The method comprises the steps of using a food-borne polypeptide with known activity as a research object, utilizing the three-dimensional quantitative structure-activity relationship technology for establishing the food-borne polypeptide antioxidant activity three-dimensional quantitative structure-activity relationship model, and adopting the MM+ method the semi-empirical quantum chemistry method AM1, the DFT method and other quantum chemistry technologies to obtain quantum chemistry parameters. According to the construction method, analysis and statistics are carried out on the food-borne polypeptide quantum chemistry parameters, the antioxidant activity sites of the food-borne polypeptide are determined, and quantitative structure-activity model is constructed by utilizing the bond length, charge distribution, frontier molecular orbit energy parameters of the activity sites and food-borne polypeptide antioxidant activity values. The constructed model can rapidly and accurately predict the activity value of the food-borne polypeptide with the unknown activity, and the relationship between the antioxidant activity and structural features can be reasonably explained; compared with a traditional high throughput screening technology, the screening efficiency is greatly improved, and the cost is reduced.