Wetlands are an important natural source of methane (CH4), so it is important to quantify how their emissions may vary under future climate change conditions. The Qinghai–Tibet Plateau contains more than a third of China’s wetlands. Here, we simulated temporal and spatial variation in CH4 emissions from natural wetlands on the Qinghai–Tibet Plateau from 2008 to 2100 under Representative Concentration Pathways (RCP) 2.6, 4.5, and 8.5. Based on the simulation results of the TRIPLEX-GHG model forced with data from 24 CMIP5 models of global climate, we predict that, assuming no change in wetland distribution on the Plateau, CH4 emissions from natural wetlands will increase by 35%, 98% and 267%, respectively, under RCP 2.6, 4.5 and 8.5. The predicted increase in atmospheric CO2 concentration will contribute 10–28% to the increased CH4 emissions from wetlands on the Plateau by 2100. Emissions are predicted to be majorly in the range of 0 to 30.5 g C m−2·a−1 across the Plateau and higher from wetlands in the southern region of the Plateau than from wetlands in central or northern regions. Under RCP8.5, the methane emissions of natural wetlands on the Qinghai–Tibet Plateau increased much more significantly than that under RCP2.6 and RCP4.5.