Abstract: This study took cyanobacteria form water source area of Jinshugang in Taihu Lake as the example, the cyanobacterial community composition in water and sediment was analyzed by high-throughput sequencing technology, and the effect of physicochemical parameters on the changes of cyanobacteria was also examined. The results showed that the composition of bacterial communities in water was similar with that in sediment, and the community structure of cyanobacteria in water changed greatly with the seasons, while the community structure of cyanobacteria in sediment changed little. The dominant families of cyanobacteria were Microcystaceae and Synechococcales, and the Microcystaceae was the largest families during the cyanobacteria bloom. Water temperature, dissolved oxygen, total nitrogen and total phosphorus were the main physicochemical factors affecting the change of cyanobacterial community structure. There were 12 genera of algae-dissolving bacteria detected in Jinshugang throughout the whole year, and the main bacteria were Pseudomonas and Flavobaeteria. The proportion of algae-dissolving bacteria was opposite to cyanobacteria bloom, the proportion of cyanobacteria in bacteria was low during cyanobacterial outbreaks and high at the beginning and ending of the outbreak. Besides, it was found that the cyanobacterial bloom in sediment took precedence over the cyanobacterial bloom in water as the air temperature increased. The phenomenon of migration and enrichment from water to sediment occurred when the proportion of cyanobacteria in water was high during the cyanobacterial bloom.