The invention discloses a method for preparing phycocyanin from fresh spirulina. The process design is based on convenience, high efficiency and capability of facilitating comprehensive utilization of different components, the fresh spirulina is used as a processing raw material, and the spirulina phycocyanin is prepared through steps of low-temperature wall breakage, ammonium sulfate fractional salting-out, polyethylene glycol 2000/(NH4)2SO4 two-aqueous-phase extraction, ultrafiltration and vacuum freezing drying. With the adoption of the method, the yield of the spirulina phycocyanin is higher, the obtained spirulina phycocyanin is low in polysaccharide content, the purity A620/A280 is about 3.7, the method is applicable to preparation of the phycocyanin from other algae used as raw materials, the biological activity of all components of the spirulina can be well kept during preparation, other obtained separated parts can be further processed, a series of products such as active polysaccharides, chlorophyll, algal protein and the like can be obtained, and the method has the high promotional value and the broad application prospect.