It has become an important measure for emergency treatment of cyanobacteria by using modified clays to control algal blooms in coastal regions and aquaculture water.However, there is less research focusing on the security risks led by toxic algae which were attached on the modified clay and left in the water. In this paper, PAC modified clay was selected for simulation experiments.The effects of applying the modified clay on the structure of cyanobacteria attached on the PAC modified clay, release and reduction of nutrients and microcystins, and the amounts of other functional bacteria (nitrifying-denitrifying bacteria) were investigated. The results showed that algae removal rate of modified clay applied in the slightly blooming water was 96.04%±0.99%. There was not a significant difference of algae removal rate inslightly blooming water and severely blooming water. Application of the modified clay effectively controlled the concentration of cyanobacteria in water for a long time. Transmission electron microscopy experiments revealed that cyanobacterial cell membrane became incomplete and the regular lamella structure was damaged after the cyanobacteria being settled with modified clay for 4 days. With the damage of cyanobacteria attached on PAC modified clay, the content of dissoloved total nitrogen in water increased rapidly, while the content of dissoloved total phosphorus could be maintained at a low concentration for a long time. With the application of PAC modified clay in water, the total bacteria number in the water was in agreement with that of the blank control, while the number of nitrifying-denitrifying bacteria decreased significantly. The releasing risks of microcystins after loading the modified clay mainly happened in the severely blooming water. The application of PAC modified clays in severely blooming water resulted in an accelerating release of MC-LR and MC-RR. The peak value of MC-LR and MC-RR amounts were 1.69±0.09 times and 2.04±0.09 times larger than that in control case,respectively. But the time of MC-LR amount reaching to the safety limit(<1 μg/L)was shortened for about 8 days, compared to the control case. In addition, the application of PAC modified clay in water did not lead to excessive concentrations of Al³⁺ and Cl^-.