Characteristics, distribution, source, and ecological risk level of polycyclic aromatic hydrocarbons (PAHs) in sediments along Yangtze River Estuary Deepwater Channel were investigated. Total concentration of fifteen PAHs of study area ranged between 89.52 and 208.02 ng/g (mean value 140.48 ng/g). PAHs ratios and the statistical analysis showed that local fossil fuels high-temperature combustion (vehicular exhaust, anthropogenic combustion and pyrogenic sources) was the main PAHs origin. According to sediment quality guidelines (SQGs) and other criteria, the potential ecological risks of PAHs in sediments along Yangtze River Estuary Deepwater Channel are at low to medium levels, but the presence of dibenzo[a,h]anthracene (DBahAnt) requires more study and evaluation of potential toxicological effects.