The invention discloses a microalgae harvesting method in process of absorbing industrial flue gas CO2 with microalgae. The microalgae harvesting method comprises following steps: 1) microalgae is cultured, and when the concentration of microalgae reaches 0.3 to 10g/L, harvesting is to be performed; 2) in harvesting, under microalgae dark conditions, the concentration of CO2 in inlet gas is increased, continuous aeration is carried out until algae liquid pH value is reduced to be lower than 7; 3) chitosan is added, and aeration is carried out until flocculation of microalgae is caused; and 4) aeration is stopped, concentration of microalgae is carried out via natural sedimentation or air floatation, and microalgae is harvested. According to the microalgae harvesting method, pre-acidification of the microalgae liquid to be harvested is carried out with high concentration CO2 in industrial flue gas, chitosan is added for flocculation of microalgae, and at last microalgae is harvested via sedimentation or air floatation; operation is simple; energy consumption is low; no secondary pollution is caused; and adding of organic or inorganic acids is not needed to achieve ideal microalgae harvesting effect.