In recent years, the water quality of water bodies in Lake Taihu Basin has improved significantly because that all provinces and municipalities in the basin have intensified their efforts in pollution governance. In Lake Taihu, the concentration of ammonia nitrogen and total nitrogen showed a significant downward trend, while a upward trend for the concentration of total phosphorus (TP). To explore the reasons for such TP increase, this paper used the measured data and remote sensing data between 2010 to 2017 from Lake Taihu Basin Authority of Ministry of Water Resources. We analyzed the correlation between the pollution load of inflow river, aquatic vegetation and cyanobacteria and the TP. The results showed that the TP in the inflow rivers was higher than those in the Lake Taihu, and TP was not easy to remove from the lake. There was a significant positive correlation between the continuous accumulation of TP loading and the epilimnetic TP in Lake Taihu. It is concluded that the basic factor of the high TP concentration is the large amount of phosphorus loading into the lake. Aquatic vegetation can absorb nutrients from lake sediments and inhibit the resuspension of sediment so as to reduce the release of endogenous nutrients. The substantial decrease of aquatic vegetation led to the increase of TP concentration in East Lake Taihu. Recently the abundance of blue-green algae in Lake Taihu showed an increasing trend. Under such circumstance, the monitoring TP also increased.