The invention belongs to the technical field of biological engineering, and specifically relates to a method for extracting protein peptide from poecilobdella manillensis. The method comprises the following steps: disinfection, grinding, coarse filtration, microfiltration, ultrafiltration, alkali dissolution, microwave treatment, centrifugation, precipitation, discoloring, enzymatic hydrolysis, precipitation, microfiltration, ultrafiltration, nano filtration, condensation, and spray drying. A physical method is used to replace a chemical method to separate acidic polypeptide so as to obtain a coarse product of acidic polypeptide; the coarse product can be used to produce Chinese patent medicine containing acidic polypeptide and purified acidic polypeptide, the separation rate is high, the activity can be well protected, no pollution is generated, and clean production is achieved.