The invention provides a preparation method of chlorella concentrate phycocyanin functional beverage and belongs to the field of biotechnology. The preparation method comprises the following steps: uniformly mixing chlorella and deionized water in a ratio of 1:(20-50), heating mixed liquor for 30-60 minutes at the temperature of 110-121 DEG C, centrifuging for 15-30 minutes, then abandoning precipitates, carrying out ultrafiltration on supernatant, and carrying out freeze drying on ultrafiltrate, so that chlorella concentrate is obtained; mixing spirulina powder and water in a ratio of 1:(10-20), swelling for 24 hours, then stirring and leaching for 2-4 hours at the temperature of 25-40 DEG C and the stirring rotating speed of 100-400rpm, centrifuging a leachate for 15-30 minutes, carryingout ultrafiltration on the supernatant for removing small molecular impurities, so that phycocyanin solution with color value of higher than 0.8 is obtained, carrying out ultrafiltration on the phycocyanin solution, and carrying out free drying on ultrafiltrate, so that phycocyanin powder is obtained; mixing the obtained phycocyanin, the chlorella concentrate, white granulated sugar, food additives such as sodium benzoate and tea polyphenol as well as water, preparing into functional beverage with health function, filtering and removing bacteria with a 0.22 Mum filter membrane, and then packaging. The preparation method provided by the invention is simple and reliable in operation, and industrial production can be carried out.