Water use efficiency (WUE) is an important variable used in climate change and hydrological studies in relation to how it links ecosystem carbon cycles and hydrological cycles together. However, obtaining reliable WUE results based on site-level flux data remains a great challenge when scaling up to larger regional zones. Biophysical, process-based ecosystem models are powerful tools to study WUE at large spatial and temporal scales. The Integrated BIosphere Simulator (IBIS) was used to evaluate the effects of climate change and elevated CO₂ concentrations on ecosystem-level WUE (defined as the ratio of gross primary production (GPP) to evapotranspiration (ET)) in relation to terrestrial ecosystems in China for 2009–2099. Climate scenario data (IPCC SRES A2 and SRES B1) generated from the Third Generation Coupled Global Climate Model (CGCM3) was used in the simulations. Seven simulations were implemented according to the assemblage of different elevated CO₂ concentrations scenarios and different climate change scenarios. Analysis suggests that (1) further elevated CO₂concentrations will significantly enhance the WUE over China by the end of the twenty-first century, especially in forest areas; (2) effects of climate change on WUE will vary for different geographical regions in China with negative effects occurring primarily in southern regions and positive effects occurring primarily in high latitude and altitude regions (Tibetan Plateau); (3) WUE will maintain the current levels for 2009–2099 under the constant climate scenario (i.e. using mean climate condition of 1951–2006 and CO₂concentrations of the 2008 level); and (4) WUE will decrease with the increase of water resource restriction (expressed as evaporation ratio) among different ecosystems.