Excessive phosphorus is the main problem of water pollution in the main stream of the Yangtze River, while it is not clear about the distribution characteristics and spatial differences of phosphorus in the urban river stretches of the middle and lower reaches of the Yangtze River. In this study, a field survey in June 2014 revealed that the average particulate phosphorus (PP) concentration ranged from 0.195 mg/L to 0.105 mg/L from Wuhan (WH) in the middle reaches of the Yangtze River to Shanghai (SH, 1081 km from WH) in the lower reaches of the Yangtze River, and the average PP-to-the total phosphorus (TP) ratio decreased from 85.71% in WH to 45.65% in SH, while the average soluble reactive phosphate (SRP) concentration ranged from 0.033 to 0.125 mg/L, and the average SRP-to-total dissolved phosphorus (TDP) ratio increased from 60.73% in WH to 88.28% in SH. In general, PP was still an important form of TP in the middle and lower reaches of the Yangtze River. The concentrations of PP and SRP at different sampling locations and water depths in the same monitoring section showed differences, which might be related to the transportation and sedimentation of suspended sediment (SS) and differences in the location of urban sewage outlets. Historical data showed that the concentration and particle size of the SS decreased over time, while the discharge of wastewater also increased over time in the Yangtze River Basin. The measured results showed that there was a significant positive correlation between SS and PP. As a result, the concentration of SRP might increase in the middle and lower reaches of the Yangtze River. If the SRP concentration is not properly controlled, the degree of eutrophication of water body could significantly increase in the Yangtze River estuary, the riparian zone of the urban river stretches, the tributary slow-flow section, and the corresponding lakes connected with the Yangtze River.