Tibetan Plateau (TP) is known as the Third Pole, yet little is known about environmental behavior and trophodynamic of PFAS in pristine ecosystem linked to accelerated glaciers melting. We characterized sediment-water partition behaviors in high-altitude region, compared trophic magnification potential between different climatic zones, and used structural equation model (SEM) to link geographic, biologic variability to PFAS bioaccumulation. Short-chained (including PFBA and PFBS) were predominant in water, whereas long-chained (6:2 FTS, PFOS) contributed more in organisms from Yarlung Tsangpo River, suggesting long-chain dependence bioaccumulation potential. Furthermore, bioaccumulation factor of C6-C10PFAS of fish even exceeded that in human-impacted area. Sigma PFAS concentrations ranged from 0.53 to 67.3 ng/g dw in various organisms (phytoplankton (mean: 3.88 ng/g) < zooplankton (5.48 ng/g) < gastropod (11.3 ng/g) < fish (29.4 ng/g)). Trophic magnification factors (TMFs) were estimated higher than 1 for long-chained PFAS (6:2 FTS, PFOS, PFDA and PFUnDA). The geographical variability and oligotrophic food web ecology accounted for discrepancies of TMFs. The declining PFAS concentrations with increasing size of specific fish species could be attributed to longer-lived, slow-growing of fish caused by growth dilution effect. SEM revealed strong impacts of biological variables adapted to geographical factors on bioaccumulation, which crucial for estimating ecological risks even in remote-areas.