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Methane (CH₄) is a potent greenhouse gas (GHG) that affects the global climate system. Knowledge about land–atmospheric CH₄ exchanges on the Qinghai-Tibetan Plateau (QTP) is insufficient. Using a coupled biogeochemistry model, this study analyzes the net exchanges of CH₄ and CO₂ over the QTP for the period of 1979–2100. Our simulations show that the region currently acts as a net CH₄ source with 0.95 Tg CH₄ y⁻¹ emissions and 0.19 Tg CH₄ y⁻¹ soil uptake, and a photosynthesis C sink of 14.1 Tg C y⁻¹. By accounting for the net CH₄ emission and the net CO₂ sequestration since 1979, the region was found to be initially a warming source until the 2010s with a positive instantaneous radiative forcing peak in the 1990s. In response to future climate change projected by multiple global climate models (GCMs) under four representative concentration pathway (RCP) scenarios, the regional source of CH₄ to the atmosphere will increase by 15–77% at the end of this century. Net ecosystem production (NEP) will continually increase from the near neutral state to around 40 Tg C y⁻¹ under all RCPs except RCP8.5. Spatially, CH₄ emission or uptake will be noticeably enhanced under all RCPs over most of the QTP, while statistically significant NEP changes over a large-scale will only appear under RCP4.5 and RCP4.6 scenarios. The cumulative GHG fluxes since 1979 will exert a slight warming effect on the climate system until the 2030s, and will switch to a cooling effect thereafter. Overall, the total radiative forcing at the end of the 21st century is 0.25–0.35 W m⁻², depending on the RCP scenario. Our study highlights the importance of accounting for both CH₄ and CO₂ in quantifying the regional GHG budget.