Based on monthly monitoring data of 31 sites in Lake Taihu from 2007 to 2019, the different environmental factors that influence the chlorophyll-a (Chl.a) concentration in the algae-dominant region (ADR) and macrophyte-dominant region (MDR) were analyzed. Both the total phosphorus (TP) and Chl.a concentrations in the ADR and MDR showed a fluctuated increasing tendency. The turning points of TP and Chl.a concentrations for the ADR and MDL were 2015 and 2016, separately. The Chl.a concentrations in the ADR and MDR had significant relationships with the lowest mean monthly water temperature, accumulated temperature before winter, mean annual water temperature, as well as mean annual wind speed. The Chl.a concentration in the MDR had significant relationships with the submerged plant coverage. Notable changes occurred in the intra-and inter-annual precipitation in the Huxi sub-region of the Taihu Basin. The relationships between the annual precipitation and the Chl.a concentration in the ADR and MDR were not significant, however, the five days extreme precipitation had strong significant positive relationships with the next year's Chl.a concentration in ADR and MDR. The cyanobacterial bloom intensity will keep the high level in recent years, which demands urgently for cyanobacteria salvage and disposal during the high-temperature period to guarantee drinking water security. Research on the non-point source pollution prevention and control measures should be strengthened in the heavy precipitation period for the Huxi sub-region of the Taihu Basin, to decrease pollutant fluxes of the rivers into Lake Taihu. The restoration measures for reducing wind-wave disturbance in the Dongshan, Xishan, and Dongjiaozui water area should be promoted as soon as possible to recover the submerged plant in these areas.