Government has strengthened the comprehensive management and restoration of the water environment in Taihu Basin. Despite the great efforts, the total phosphorus concentration in Lake Taihu rebounded in 2015-2016. Occurrence of cyanobacterial blooms has not been effectively inhibited. Thus, this essay is going to examine the reasons behind and figure out the key direction in controlling the total phosphorus in Lake Taihu. The water quantity balance analysis and the total phosphorus mass balance analysis will be carried out through the calculation of the total phosphorous fluxes and the water flows between Lake Taihu and the surrounding rivers. Affecting factors, including rainfall, lake storage regulation and human factors, will also be considered. Based on the analysis, we will investigate the sources of total phosphorus change in Lake Taihu as well as the reasons of variations. The results showed that Taihu Basin had abundant rainfall in 2015-2016, especially in 2016, there was a severe basin flooding. The maximum water level of Lake Taihu reached 4.87 m, only 0.1 m lower than that of the historical record in 1999. Enormous total phosphorus load flowed from the surrounding rivers to Lake Taihu, which became the main external source of Lake Taihu's total phosphorus load. The load from rivers occupied 66.8% and 74.2% of the annual total phosphorus load in Lake Taihu in 2015 and 2016, respectively. On the other hand, for internal source, the massive reduction of submerged plants played an important role in affecting the total phosphorus concentration in Lake Taihu. The area of submerged aquatic plants in Lake Taihu decreased by 88.7% in 2015. The large-scale harvest of aquatic plants hindered the phosphorus absorption and transformation capacity of the lake. In 2015 and 2016, the total phosphorus load retained in Lake Taihu accounted for 21.5% and 27.5% of the total phosphorus load. The increase in total phosphorus concentration in Lake Taihu provided a strong foundation for cyanobacterial blooms. It is urgent to lower the amount of total phosphorus into Lake Taihu and tighten the control of the total phosphorus sources.