The ability of roots to take up water depends on both root distribution and root water uptake efficiency. The former can be experimentally measured, while the latter is extremely difficult to determine. Yet a correct representation of root water uptake process in land surface models (LSMs) is essential for a correct simulation of the response of vegetation to drought environment. This study evaluates the performance of the Common Land Model (CLM) to reproduce energy and water vapour fluxes measured with an eddy covariance system in a Central Asian desert ecosystem. The default CLM appears to be able to reproduce observed net radiation, soil subsurface temperature, and wet period latent (Qle) and sensible heat (Qh) fluxes, but significantly underestimate Qle and overestimate Qh during dry period. Underestimation of Qle is attributed to the inappropriate representation of root water uptake process in the CLM model. Modifying the original root water uptake function (RWUF) with a linear function of soil water potential to one with an exponential function significantly improves the performances for both Qle and Qh. The net radiation and ground heat flux simulations did not change noticeable with the new RWUF. It is concluded that an exponential RWUF is a valuable improvement of the CLM model and likely for other similar LSMs that use a linear RWUF for Central Asian desert ecosystems.