This paper reports the study of Coptis extract on its inhibition of Microcystis aeruginosa in the laboratory, and its influence on the growth of phytoplankton and zooplankton, and its impact on the Microcystin, in the natural water. The results show that: (1) the Coptis extract has obvious inhibitory effect on the Microcystis aeruginosa, and the effect increases with time. The inhibitory rate keeps above 85% from the 3rd day to 13th day after adding the Coptis extract; (2) In the natural water, the Coptis extract does not change the dominant species of phytoplankton and the species composition of zooplankton. 1~9 days after adding the Coptis extract, the density of phytoplankton cells and the dominant species (Cyanophyta) cells decrease, and the quantity of poor-middle nutrition species zooplankton soars to rise rapidly. (3) No variation on Microcystin-LR content in experiment area is observed one day after adding Coptis extract.