The invention discloses a method for extracting a phycocyanin from a microcoleus vaginatus, which comprises the following steps: preparing the microcoleus vaginatus culture medium with a sodium nitrate, a potassium phosphate dibasic, a magnesium sulfate, a calcium chloride, a citric acid, a ferric ammonium citrate, an EDTA, a sodium carbonate and a trace element solution according to a certain proportion, culturing the microcoleus vaginatus in the culture medium and making the microcoleus vaginatus powder, extracting a phycocyanin from the microcoleus vaginatus powder and purifying the phycocyanin. The method for extracting a phycocyanin from a microcoleus vaginatus has the advantages of simplicity, convenient operation, safety and reliability, high yield, good product quality and simple operated equipment, which is suitable for industrial production.