Surface sediments were obtained from a matrix of 76 sample sites in the inner shelf mud belts of the East China Sea (ECS) for a comprehensive study of the distribution, composition, deposition flux, and fate of polycyclic aromatic hydrocarbons (PAHs). The sampling sites covered an area of ~80,000 km2 extending ~1000 km from the mouth of the Yangtze River to the Min River in the inner shelf. The total deposition flux of the 16 USEPA priority PAHs (16 PAHs) of the Yangtze estuarine-inner shelf was estimated to be 152 t/yr, accounting for ~38% of the total annual input of the 16 PAHs into the ECS. This indicates that the Yangtze estuarine-inner shelf is one of the largest sinks of land-based PAHs in the world. Principal component analysis indicated that the 16 PAHs in the northern Yangtze estuarine mud area were mostly phenanthrene while shifting to high-molecular-weight PAHs in the southern Min-Zhe coastal mud area. The positive matrix factorization model revealed that the deposition flux of low-molecular-weight (LMW) PAHs decreased from north to south, most likely due to the mass transfer between the resuspended sediments triggered by the East Asian monsoon and the water columns, as the resuspended sediments are transported southward. This release of LMW PAHs from the sediments to the water columns could become an important secondary PAH source in ECS.