Methane (CH4) emissions from thawing permafrost could amplify climate warming. However, long-term trajectory of net CH4 balance in permafrost regions, particularly high-altitude permafrost regions, remains unknown. Based on literature synthesis and CLM5.0 model, we evaluate the contemporary and future CH4 fluxes across the Tibetan alpine permafrost region from 1989−2100. Here, we find that this permafrost region functions as a marginal CH4 sink during 1989-2018 (−0.01 ± 0.01 Tg CH4 yr⁻¹), and future trajectories diverge, with warming and wetting under low- and medium-emission scenarios (SSP1-2.6/SSP2-4.5) driving persistent CH4 emissions (0.07 Tg CH4 yr⁻¹). By contrast, under higher emission scenarios (SSP3-7.0/SSP5-8.5), the region shifts to net emissions by mid-century but enhanced atmospheric CH4 concentrations strengthen sink, returning it to a net sink by century’s end (−0.06 ~ −0.02 Tg CH4 yr⁻¹). These results demonstrate that climate change and atmospheric CH4 dynamics jointly mediate the trajectory of alpine permafrost CH4 balance.