Microcystis waterbloom always occurs in colonial forms in natural waters. However, most laboratory studies on removal of Microcystis cells by various approaches were performed by using single-cell Microcystis strains. This study aimed to remove Microcystis aeruginosa, as the dominant species in Chinese waters, by Chitosan and Polymeric Aluminum Chloride (PAC) modified clays(Kaolin). Using colonial Microcystis aeruginosa strain HAB 657, the relationships between the quantity of the chitosan modified clays(y) and OD680(x) and between the quantity of the chitosan modified clays(y) and the concentration of chlorophyll-a(Chl.a)(x) was expressed as y=0.0349x-0.0019 and y=0.0524x-0.009, respectively. While relationships between the quantity of the PAC modified clays(y) and the OD680(x), and between the quantity of the PAC modified clays(,) and the Chl.a(x) content were expressed as y=0.0351x+0.0065 and y=0.0676x-0.0059 respectively. It showed that the optimal pH ranged from 5 to 8 for chitosan modified clays to remove Microcystis cells, and PAC modified clays with 5-9 optimal pH. Analysis of Electron Transport Rate (ETR) showed that sedimented Microcystis cells became yellowish and decayed in a week after treatment by PAC modified clay, and were dead in one month after the treatment of chitosan modified clays.