In recent years, due to unsustainable production methods and the demands of daily life, the water quality of the Yangtze River has deteriorated. In response to Yangtze River protection policy, and to protect and restore the ecological environment of the river, a two-dimensional model of the Jiangsu section was established to study the water environmental capacity (WEC) of 90 water environment functional zones. The WEC of the river in each city was calculated based on the results of the water environment functional zones. The results indicated that the total WECs of the study area for chemical oxygen demand (COD), ammonia nitrogen (NH3-N), and total phosphorus (TP) were 251,198 t/year, 24,751 t/year, and 3251 t/year, respectively. Among the eight cities studied, Nanjing accounted for the largest proportion (25%) of pollutants discharged into the Yangtze River; Suzhou (11%) and Zhenjiang (12%) followed, and Wuxi contributed the least (0.4%). The results may help the government to control the discharge of pollutants by enterprises and sewage treatment plants, which would improve the water environment and effectively maintain the water ecological function. This research on the WEC of the Yangtze River may serve as a basis for pollution control and water quality management, and exemplifies WEC calculations of the world’s largest rivers.