The water and sediment conditions have been changed by the establishment and operation of the cascade reservoirs in the upper reaches of the Yangtze River, resulting in the disruption of natural hydrological rhythm. The transports of water-sand-phosphorus have been transformed into imbalanced and discontinuous, as well as alterations in the flux and occurrence form of total phosphorus. Furthermore, under the influence of water level regulation, sediment interception and reservoir thermal stagnation, the river runoff, sediment, temperature has changed, producing a series of regional ecological environment effects. In view of the total phosphorus in the Yangtze River, especially the variation of runoff, sediment, water temperature and phosphorus transport caused by the construction and operation of water conservancy project, this paper reviewed the new situation of the Yangtze River basin from the aspects of the spatial pattern of water-sediment, as well as the migration and transformation characteristics of phosphorus in the Yangtze River. Meanwhile, the influence of runoff-sediment-temperature change on phosphorus transport was analysed. Based on the deficiencies of total phosphorus monitoring and management, it was recommended to strengthen the connection between total phosphorus standards in rivers, lakes and reservoirs, improve the environmental standard system of total phosphorus, promote the study of water quality benchmark, enhance the formulation of local and watershed standards, and adhere to the dual control of total phosphorus emission concentration and total load. These measures will ultimately contribute to the effective resolution of total phosphorus issues.