The invention discloses a flocculating agent for microalgae capture, a preparation method and applications thereof, wherein the flocculating agent comprises a cationic starch substrate and condensed tannin grafted on the substrate, and the grafting degree of the condensed tannin on the substrate is 4-20%. The preparation method comprises: cationizing starch, and grafting condensed tannin on the cationized starch. According to the invention, in actual microalgae capture, when the use amount of the flocculating agent is 0.5-0.7 mg/L, the microalgae harvesting rate can reach more than 90%; and compared with starch and cationic starch, the flocculating agent of the invention has the following characteristics that the harvesting rate is greatly increased, the use amount of the flocculating agent can be reduced by more than 40 times or above, and the economic benefits are remarkable.