An in-situ enclosure experiment was conducted to study the effect of harvesting of algae on cyanobacteria growth and water quality in the northwestern Lake Chaohu in autumn. The gill type filter was used to harvest cyanobacteria in two enclosures and no treatment was conducted in control enclosure. The growth rates of cyanobacteria and the concentrations of nutrients and organic matters were investigated after harvesting compared with that in the control. The initial concentrations of chlorophyll-a, total nitrogen and total phosphorus reached 309.5±3.7 μg/L, 3.32±0.14 mg/L and 0.30±0.04 mg/L, respectively. Algogenic organic matter became a major source of dissolved organic matter in the enclosures, and fluorescent dissolved organic matter was dominated by proteinoid materials. Harvesting reduced the cyanobacterial biomass by 41.7%, which relieved the "density dependence of growth" of cyanobacteria, and then resulted in an increase in diel frequency of dividing cells and the in-situ growth rates of cyaobacteria. Algogenic organic matters were reduced due to harvesting increased the viability of cyanobacterial cells in a short term. What's more, cyanobacteria tended to decline in autumn and chlorophyll-a concentration dropped gradually in the enclosures, which testified that harvesting in autumn would not cause a second outbreak of algal bloom. Primary productivity, nitrogen and phosphorus nutrients, Potassium permanganate index were controlled significantly in the harvesting enclosures due to the reduction of cyanobacterial biomass. Furthermore, the release of algogenic organic matters was controlled and macromolecular organic compound was degraded easily to low-molecular-weight organics. Therefore, harvesting the accumulated cyanobacteria shoreside in autumn could control the amount of algae, nitrogen and phosphorus nutrients as well as the release of algogenic organic matters, which could reduce the ecological risk in lakes.