The invention discloses a method for simultaneously separating high-purity 
phycocyanin and 
allophycocyanin and application thereof. The method comprises the following steps of: repeatedly freezing and thawing spirulina 
dry powder, ultrasonically crushing, and centrifuging, wherein supernate is a crude 
phycobiliprotein extracting solution; then adding 
ammonia sulfate, and taking out the supernate when the saturation degree is 25-35%; then, adding 
ammonia sulfate, taking out precipitates when the saturation degree is 60-70%, dialyzing for 
precipitation to obtain a primarily purified 
phycobiliprotein extracting solution, and loading the primarily purified 
phycobiliprotein extracting solution to a hydroxyapatite column; and collecting 0.02-0.03M 
phosphate buffered solution which contains 0.1-0.2M 
sodium chloride and has the pH value of 6.5-7.2, and 0.1-0.12M 
phosphate buffered solution which contains 0.1-0.2M 
sodium chloride and has the pH value of 6.5-7.2, wherein the 0.02-0.03M 
phosphate buffered solution is 
phycocyanin and the 0.1-0.12M phosphate buffered solution is 
allophycocyanin. The method disclosed by the invention can be used for simultaneously preparing 
phycocyanin with a purification factor reaching 4.5 and 
allophycocyanin with a purification factor reaching 3 as well as analogues containing 
selenium and 
tellurium, and the purification scale of the method is amplified so as to acquire high-purity 
protein of a 
gram level through primary 
chromatography, so that the purification cost is greatly reduced, and the method can be used for producing the phycocyanin and the allophycocyanin.