Perfluoroalkyl substances (PFASs) are known to be persistent and toxic, and can be accumulated and trophic magnified in the environments. PFASs are widely distributed, and their coastal input poses a threat to the health of aquatic organisms and local residents. In present study, 17 PFASs including one emerging polyether substitute in water, sediment, and organisms were investigated from the South China Sea. Perfluorobutanoic acid (PFBA) was predominant in water, of which concentration ranged from ND to 10.26 ng/L, with a mean of 5.21 ng/L. Similar to sediment and organisms, PFBA was the substance with the highest concentration detected among PFASs. This result seemingly indicated that use of short-chain PFASs as substitutes for long-chain PFASs in recent years. Trophic magnification factors (TMFs) of PFASs were estimated in the marine food web. TMFs > 1 was observed only in perfluorooctane sulfonic acid (PFOS), indicating a biomagnification potential of PFOS in the given ecosystem. The estimated daily intake (EDI) of PFOS and PFOA were most prevalent in mollusk, whereas the EDI of PFBA was greater in fish and shrimp. The hazard ratio (HR) reported for seven dominant PFASs were lower than 1, which suggests that PFASs via seafood consumption would not cause significant health risk to local residents.