To study the carrying capacity of water function areas in Jiangxi province, 178 important rivers and lakes were selected as study areas. According to the underlying conditions, the water quality and the water self-purification ability in the water function area, the carrying capacity was calculated through establishing the mathematical model of water quality and setting the design flow and other related parameters reasonably. Then the program was proposed combined with the current conditions about sewage into rivers, which was used to control the amounts of total pollutants of water function areas in 2015, 2020 and 2030. It could provide valuable references for the protection and management of water resources in Jiangxi province.