The carbon use efficiency (CUE) of ecosystems, expressed as the ratio of net primary production (NPP) and gross primary production (GPP), is extremely sensitive to climate change and has a great effect on the carbon cycles of terrestrial ecosystems. Climate change leads to changes in vegetation, resulting in different CUE values, especially on the Qinghai-Tibet Plateau, one of the most climate-sensitive regions in the world. However, the changing trend and the intrinsic mechanism of climate effects on CUE in the future climate change scenario are not clear in this region. Based on the scheme of the coupled model inter comparison project (CMIP6), we analyze the simulation results of the five models of the scenario model inter comparison project (ScenarioMIP) under three different typical future climate scenarios, including SSP1-2.6, SSP3-7.0 and SSP5-8.5, on the Qinghai-Tibet Plateau in 2015–2100 with methods of model-averaging to average the long-term forecast of the five several well-known forecast models for three alternative climate scenarios with three radiative forcing levels to discuss the CUE changes and structural equations modeling (SEM) approach to examine how the trends in GPP, NPP, and CUE related to different climate factors. The results show that (1) GPP and NPP demonstrated an upward trend in a long time series of 86 years, and the upward trend became increasingly substantial with the increase in radiation force; (2) the ecosystem CUE of the Qinghai-Tibet Plateau will decrease in the long time series in the future, and it shows a substantial decreasing trend with the increase in radiation force; and (3) the dominant climate factor affecting CUE is the temperature of the factors included in these models, which affects CUE mainly through GPP and NPP to produce indirect effects. The temperature has a higher comprehensive effect on CUE than precipitation and CO2 , which are negative effects on CUE on an annual scale. Our finding that the CUE decreases in the future suggests that we must pay more attention to the vegetation and CUE changes, which will produce great effects on the regional carbon dynamics and balance.