This study argued for the first time that 6:2 chlorinated polyfluorinated ether sulfonate (6:2 Cl-PFESA) and perfluorooctanesulfonic acid (PFOS) might have different tissue distribution mechanisms in wild fish species. Nine emerging and legacy per- and polyfluoroalkyl substances (PFASs) were detected in the water and wild fish tissues samples collected from the Qiantang River. Perfluorooctanoic acid (213 ng/L) was the predominant PFAS contaminant, and the other contaminants included perfluorohexanoate (19 ng/L), perfluorobutanoate (199 ng/L) and hexafuoropropylene oxide dimer acid (55 ng/L), which are the main fluorinated alternatives used in various industries located along the Qiantang River. Furthermore, PFOS (742 ng/g) and 6:2 Cl-PFESA (9.0 ng/g) were the predominant PFAS contaminants detected in the fish tissue samples. The differences in the potential molecular mechanism of the tissue distribution of PFOS and 6:2 Cl-PFESA in wild fish species are discussed. Additionally, we hypothesize that phospholipid partitioning is the primary mechanism underlying the tissue distribution of PFOS, and that a specific protein-binding mechanism is involved in the tissue distribution of 6:2 Cl-PFESA.