The paper compares the effects of three methods of phycocyanin extraction buffer and tries to find out which method is the best. Cultured Microcystis aeruginosa and cyanobacteria blooms water samples of Lake Chaohu were used as extract objects. By repeated freezing and thawing method, cyanobacterial cells were broken, and then applied with Asolctin-CHAPS buffer, phosphate buffer and Tris-HCl buffer solution as extractant agent for extracting phycocyanin. Finally, spectrophotometry was used to detect the content of phycocyanin. We analyzed the absorption spectrum of the phycocyanin extract, the concentration of phycocyanin and the relevance between phycocyanin concentration and chlorophyll-a concentration to compare the quality of three methods. Absorption spectra show that all the characteristic absorption peaks of phycocyanin are emerged at 620 nm. Experimental results show that AC buffer and PBS buffer are better than the Tris-HCl buffer in extraction efficiency. In comparison, AC buffer is more expensive and difficult to obtain and save than the other two buffers, which makes it not suitable for large-scale use. So we recommend PBS buffer as the normal buffer which can meet the requirements of large-scale water quality monitoring.