Enhanced riverine nitrogen (N) and phosphorus (P) exports have greatly shaped downstream nutrient’s structure and induced unpleasant ecosystem effects. The regime of river nutrients fluxes is largely unknown due to its numerous influencing factors and complex components. Long term of daily fluxes along multiple sections of the Yangtze River of China were estimated to apportion the flux into different components. High flux, middle flux and low flux based on frequency analysis are firstly used in this study to investigate nutrients flux regime dynamics. Results showed that: the increase trend of riverine N and P fluxes from upstream to downstream can be inverted by retention effect from dam and lakes, which is more significant for P and high flux component. Nutrient fluxes in upstream are mainly comprised of high flux while middle and low flux dominate the downstream. Significant change trend was observed for all nutrients flux components along the river differs. Both middle and low flux percentage are increasing significantly while high flux percentage decrease, suggesting that hedging effect intensifies from tributaries in the downstream. The Three Gorges dam has a significant retention effect on N and P fluxes, especially for high flux and TP. The net change of N and P fluxes along the Yangtze River do not coincide in space, indicating that there is heterogeneity between the source and sink of N and P in the river. The inconsistent alteration between riverine total nutrients flux and its components indicates that more attention should be paid to flux structure for better mitigation measures.