Abstract: Per- and polyfluoroalkyl substances (PFASs), as important new pollutants, have attracted much attention due to their negative environmental and health effects. Since the coastal environmental quality affects the water quality and seafood safety of coastal residents, it is necessary to pay attention to the ecological risk of estuarine and coastal PFASs. This paper summarized the occurrence, migration, transformation, and ecological risk of PFASs in the marine environment of Xiamen and analyzed the evolution trend of PFASs. The results show that the concentration and composition of PFASs in the water environment of the Jiulong River estuary and Xiamen sea area were affected by the runoff, rainfall, sewage discharge, and production structure, and had obvious seasonal differences. The highest concentration in 2022 appeared in summer, while in previous years it appeared in spring. The concentrations of traditional PFASs, such as perfluorooctanoic acid (PFOA), perfluorooctane sulfonic acid (PFOS), and perfluorohexane sulfonic acid (PFHxS), had not changed by orders of magnitude in recent years. The increased concentration of short-chain perfluorosulfonic acids (PFSAs) as a substitute for highly toxic compounds PFOS indicated that short-chain PFASs products are now being produced used and discharged into the sea. The concentration of PFASs in sediments had not changed by orders of magnitude in recent years, but the detection rate of short-chain PFSAs had increased, and the relative abundance of PFOS was higher than that in water. PFASs in fish were mainly PFOS and PFOA, and their ecological risk was low. Shipyards, electroplating factories, textile factories, Gaoqi Airport, and sewage treatment plants near Yudzhenzhou and its upstream area at the Jiulong River Estuary and the West Sea area of Xiamen north of the Haicang Bridge may be potential sources of PFASs pollution.