Cyanobacterial bloom has become the focus of all over the world because of its ecological risk and drinking water crisis. There are many reasons contribute to the cyanobacterial bloom in Lake Taihu. The characteristic of cyanobacteria themselves is the internal causes. As a subtropical shallow lake, Lake Taihu provides suitable temperature and hydrodynamic condition for the cyanobacterial bloom due to its geographical and hydrological meteorological characteristics. The shift from grass-shaped to algae-shaped ecosystem and the input of high load nitrogen and phosphorus nutrients are beneficial to the growth of cyanobacteria. In addition, the quadruple cycle of nitrogen and phosphorus intensifies cyanobacterial bloom. Cyanobacterial bloom interacts aqueous nitrogen and phosphorus concentrations. In order to control bloom in Lake Taihu, we should increase the output of nutrients based on cutting off the source of nitrogen and phosphorus. Above all, it is the key of ecological restoration of Lake Taihu to sequester and strengthen the recovery of macrophytes so that the macrophyte and algal ecosystems can be reconstructed.