To avoid the disadvantage that artemisinin granules coated with millimeter level chitosan alginate are easy to settle and improve the dispersion of granules in water, improved artemisinin sustained release granules (ASGs) were prepared by ultrasonic technology combined with ion crosslinking method in this study. The release kinetics of two kinds of granules under different media conditions (temperature, ionic strength, pH, algal liquid, and Taihu Lake water) were studied. The physicochemical characterization showed that the diameter and zeta potential of the improved ASGs were 1189.5nm and -38.0mV, respectively. Here, the drug release of chitosan-coated artemisinin alginate granules is affected by the temperature, pH, and ionic strength of the release medium. Whether ASGs or improved ASGs, drug release increased with the increase of temperature and ionic strength, but decreased with the increase of pH. More importantly, the release kinetics study showed that the release mechanism of the improved ASGs in Taihu Lake water and algae liquid is matrix dissolution, while the release of ASGs in Taihu Lake water was controlled by diffusion and skeleton dissolution. The growth experiment of cyanobacteria showed that the improved ASGs have a long-term inhibitory effect on algae cells, and the inhibitory effect on cyanobacteria increased with the increase of dosing concentration. Our study clearly shows that the granules with reduced diameter have the characteristics of rapid dispersion and continuous release, and have the potential to be applied to the control of cyanobacteria bloom.