With the increasing restrictions and concerns about legacy poly- and perfluoroalkyl substances (PFAS), the production and usage of alternatives, i.e., perfluoroalkyl ether carboxylic acids (PFECAs), have risen recently. However, there is a knowledge gap regarding the bioaccumulation and trophic behaviors of emerging PFECAs in coastal ecosystems. The bioaccumulation and trophodynamics of perfluorooctanoic acid (PFOA) and its substitutes (PFECAs) were investigated in Laizhou Bay, which is located downstream of a fluorochemical industrial park in China. Hexafluoropropylene oxide trimer acid (HFPO-TrA), perfluoro-2-methoxyacetic acid (PFMOAA) and PFOA constituted the dominant compounds in the ecosystem of Laizhou Bay. PFMOAA was dominant in invertebrates, whereas the long-chain PFECAs preferred to accumulate in fishes. The PFAS concentrations in carnivorous invertebrates were higher than those in filter-feeding species. Considering migration behaviors, the ∑PFAS concentrations followed the order oceanodromous fish < diadromous fish < non-migratory fish. The trophic magnification factors (TMFs) of long-chain PFECAs (HFPO-TrA, HFPO-TeA and PFO5DoA) were >1, suggesting trophic magnification potential, while biodilution for short-chain PFECAs (PFMOAA) was observed. The intake of PFOA in seafood may constitute a great threat to human health. More attention should be given to the impact of emerging hazardous PFAS on organisms for the health of ecosystems and human beings.