Based on the monthly water quality and hydrology data from 2003 to 2017, the variation characteristics of total phosphorus (TP) was investigated in the four periods which were divided by the different impoundment feature of the Three Gorges Reservoir after 2003. In the initial water impoundment process, the phosphorus retention effect of the Three Gorges Dam began at 2005. During the trial impoundment period, a marked decrease was observed in annual mean TP concentration along the main stream of the reservoir in 2008. Since then, the TP concentration in Qingxichang section was affected due to the inflow of Wu River with the high TP concentration. At the water level of 175m, there was a dramatic decrease in annual mean TP concentration from Tongguanyi sections to Guandukou section except Qingxichang section. After the operation of cascade hydropower stations upstream, a marked reduction of annual mean TP concentration happened along the main river channel sections except Guandukou section. A higher annual mean concentration of TP in Guandukou section than that in Tuokou section was observed for the first time in 2016. Meanwhile, the average concentration of TP in the flood season was no longer significantly higher than that in the dry season. In this period, no significant correlation was found between the concentration of TP and the water flow discharge in almost sections. In addition, no significant correlation was found between the concentration of TP and suspended volatile matters (SS) in Zhutuo, Tongguanyi and Guandukou section.