Abstract: The monitoring data from 2001 to 2015 were analyzed in order to understand the trend of TP concentrations at the exit and entry section in Chongqing segment of the Three Gorges Reservoir Area. Based on the investigation of pollution sources and flux calculation, the input and output balance of TP load was established in Chongqing segment,and the main sources were judged. Results showed that TP concentrations in Zhutuo section and Peishi section both were rising from 2001 to 2015. TP loads in Chongqing segment mainly originate from the input load of the Yangtze River and the Wujiang River. TP loads from pollution sources account for 12% of output load at Peishi section. In order to guarantee the water quality safety in the Three Gorges Reservoir Area and to efficiently control TP concentration, it is imperative to promote comprehensive water quality management in this watershed and develop joint pollution prevention and control strategies among all provinces along the upstream and downstream.