The invention provides a method for extracting phycobiliprotein from spirulina. The method comprises the following steps: adding water into spirulina mud to obtain a spirulina cell suspension, performing ultrasonic treatment to obtain spirulina lysate, centrifuging the lysate and taking the lysate, sequentially filtering through filter membranes which are respectively 0.8mu m and 0.45mu m, to obtain phycocyanin crude extracting liquid, then sequentially ultrafiltrating the crude extracting liquid through an ultrafiltration membranes with molecular weight cut-off of 300KD and 100KD, collecting a filtrate of the molecular section, and performing freezing and drying to the filtrate to obtain phycobiliprotein powder. According to the method, the defect of using chemical reagent to extract phycobiliprotein in the prior art is overcome, no residuals exist in the preparation, and the environment pollution does not exist. The extraction rate of the phycobiliprotein is greater than 80%, the content of phycobiliprotein is more than 60%, and the purity of the phycobiliprotein is more than 1.5. The overall technological process is safe and reliable, fast and efficient. Compared with the traditional method, by using the method, the content of the phycobiliprotein is high before using of chromatography, the phycobiliprotein with the purity not only can meet the requirement of food and cosmetic industries, but also can be applied to aspects of medical and health products, and the like.