The ecological environment of the Yangtze River and the Han River is related to the sustainable development of China's economy and society, which has always been the concern of the whole society. Total phosphorus has become the primary pollution indicator of the Yangtze River. According to the current situation of total phosphorus pollution in the Yangtze River Basin and the Han River Basin, the temporal and spatial distribution characteristics of total phosphorus concentration are compared and analyzed. The causes of total phosphorus pollution in the Yangtze River and the Han River are analyzed from the aspects of the natural geological factors, phosphorous chemical enterprise distribution, municipal domestic sewage and rural non-point source pollution. This paper can provide a scientific reference for the implementation of projects such as Water Supply Project from the Yangtze River to the Han River.