The invention relates to a preparation method for a phycocyanin polypeptide, which includes the following steps: phycocyanin is added with water for being stirred to be sufficiently dissolved, so that a phycocyanin solution is obtained; the phycocyanin solution is added with papain or neutral protease, uniform stirring is carried out and then ultrasonical treatment is carried out for 30 to 50 minutes, so that an enzymolysis product is obtained; the enzymolysis product is heated to 85 DEG C to 95 DEG C which is kept for 5 to 15 minutes, and after enzyme deactivation, cooling and centrifugation, supernatant, i.e. enzymolysis liquid, is extracted; ultrafiltration treatment is carried out on the enzymolysis liquid, so that an ultrafiltrate is obtained; the ultrafiltrate is concentrated under vacuum, and after spray-drying treatment, the phycocyanin polypeptide is obtained. The preparation method for the phycocyanin polypeptide adopts ultrasound-assisted enzymolysis, ultrasonic waves have a cavitation effect, produced air bubbles are squeezed to break to instantly produce extremely strong mechanical shear force, so that protein is degraded or protein conformation is changed, consequently, more hydrophilic groups are promoted to expose, the solubility of phycocyanin in water is increased, the binding between enzyme and phycocyanin substrate is benefited, and the efficiency of enzymolysis of phycocyanin can be remarkably increased.