The invention discloses a method for extracting selenium polypeptide from selenium-rich passion fruit seeds. The method comprises the following steps: taking out, cleaning and drying selenium-rich passion fruit seeds, performing crushing and sieving, carrying out ultrasonic treatment, carrying out ultrasonic action to separate grease in a mixed solution, centrifugally removing oil, performing precipitating to obtain a protein mixture in the passion fruit seeds, performing homogenizing to turn proteins into a stable system, carrying out enzymolysis by using an immobilized enzyme, and carrying out centrifugal separation to obtain the purified selenium-containing polypeptide mixture of the passion fruit seeds. According to the method, the selenium polypeptide in the passion fruit seeds can berapidly extracted and utilized. Compared with traditional methods, the method has the advantages of easy operation, low cost and high extraction recovery rate, and the extracted selenium polypeptideis good in quality and remarkable in economic value effect.