The invention relates to a method for comprehensively utilizing and processing spirulina, and belongs to the technical field of food processing. The method comprises the following steps of: pretreating, extracting and separating the spirulina, preparing phycocyanin peptide from primary extracting solution through compound enzymolysis, preparing spirulina protein peptide from spirulina residues through the compound enzymolysis, and preparing spirulina polysaccharide from an ultrafiltration concentrated solution through refining and impurity removal. According to the method disclosed by the invention, molecular weight distinguishing of protein and polysaccharide is realized in an enzymolysis mode, meanwhile, by means of the distribution difference of the phycocyanin and the spirulina protein in cell tissues, the soluble phycocyanin is firstly dissolved out in a crushing extraction mode so as to realize separation of the phycocyanin in the extracting solution and the protein in cell walls, and then, the extracting solution and the spirulina residues are respectively subjected to enzymolysis to obtain two products, namely the phycocyanin peptide and the spirulina protein peptide. According to the method disclosed by the invention, the use of organic reagents is avoided, the extraction step of comprehensive utilization of the spirulina product is simplified, and the comprehensive utilization value of spirulina resources is improved.