This work is the first comprehensive survey of the Yangtze River, covering its origin to the estuary mouth. It focuses on the geographical and industrial factors influencing the distribution of polycyclic aromatic hydrocarbons (PAHs) in sediments, along with their contamination levels, sources, and ecological risks. The total concentrations of PAHs ranged from 2.14 to 796 (mean 179 +/- 179) ng/g, which falls within the low-to-middle range compared to global levels. Four-ring PAHs were observed with the highest proportion (34.0%), followed by three-rings (24.7%), five-rings (16.0%), two-rings (16.6%), and six-rings (8.62%). PAH levels were significantly higher downstream of the confluences of the Yangtze mainstream and its major tributaries, as well as in areas with frequent industrial activity. Heavy metals (Zn, Pb, and Cd) and industry output values were positively correlated with PAHs concentrations, especially three-ring PAHs. The results of source analysis, based on molecular diagnostics and principal component analysis, identified coal, biomass, and petroleum combustion as the main sources of PAHs. Among these, industrial coal combustion and vehicle emissions were dominant, contributing 39% and 64% of the PAHs pollution in top and bottom sediments, respectively. The toxicity equivalence (TEQ) evaluation results showed that the total TEQ of & sum;16PAHs (mean: 14 ng/g) was below the 600 ng/g TEQBaP standard established by the Canadian Council of Ministers of the Environment. BaP had the highest TEQBaP, followed by DahA and BbF. The risk assessment indicated that Nap and Pyr were the two congeners with the highest risk, accounting for 24-33% and 21-28% of the Risk Quotient for negligible concentration values (RQNCs) and maximum Permissible Concentration values (RQMPCs) of & sum;16PAHs, respectively. Despite the overall low to moderate risks of PAHs in the region, the above-mentioned major compounds (e.g., BaP, DahA, BbF, Nap, and Pyr) should be of continued concern.