Rapid urbanisation, due to an imbalance in fitness with technological levels, has resulted in the accumulation of phosphorus (P) in river sediments, which is prone to environmental problems such as eutrophication of water bodies. However, little is known about phosphorus's geochemical composition and environmental risks in the natural-rural-suburban-urban river sediment continuum, which is an urgent need. This study investigated the concentration and fractionation of P using sequential P extraction and their influencing factors by introducing the PLS-SEM model (Partial Least Squares Structural Equation Model) along this continuum from the Qinhuai River. The results showed that the sedimentary TP concentrations and P fractions nearly increased dramatically with increasing the urbanization gradient. This spatial heterogenicity of P along a river was attributed mainly to land use patterns and sediment properties (nutrients >metals > grain size). In addition, the highest values of TP, BAP (biologically active P) and PPI (P pollution index) were found in urban sediments among four regions, indicating a higher environmental risk of P release, which may increase the risk of eutrophication in overlying water bodies. Collectively, this work improves the understanding of the spatial dynamics of P in the natural-rural-urban river sediment continuum, highlights the need to control P pollution in urban sediments and provides a scientific basis for the future usage and disposal of P in sediments.