The invention discloses an environment-friendly microalgae collecting method. According to the method, microalgae is cultured into the concentration of 0.5 g/L-1.5g/L in a microalgae bioreactor, 80% of a microalgae culture solution is transferred into a flocculation reaction tank through a pipeline or a pump, a cationic starch solution with a substitution degree of 0.15-0.45 is added into the microalgae culture solution and is taken as a flocculating agent, the wet to dry weight ratio (w/w) of a cationic starch mass to the microalgae in the solution ranges from 0.01 to 0.20, the microalgae culture solution is stirred for 5-10 minutes at the rotation speed of 200 r/min to promote the microalgae to flocculate, the microalgae culture solution is subjected to static settlement for 10-30 minutes, a sedimentary microalgae concentrated solution is collected, and a liquid supernatant is circularly used for re-cultivating the microalgae. According to the environment-friendly microalgae collecting method, the cationic starch solution is taken as the flocculating agent, so that the method has the characteristics of non-toxicity, economy, environmental protection, high flocculation efficiency and the like, flocculated microalgae is dense, the enrichment factors are high, original biological characteristics of the microalgae can be better kept, and the microalgae can be directly used in the fields of food, feed, biodiesel and the like.