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The Central Asia region is covered by vast desert ecosystems, where the characteristic of energy and water fluxes is different from other humid ecosystems. The application of land surface models (LSMs) in arid and semiarid ecosystems was largely limited. This paper presents a detailed evaluation of Common Land Model (CoLM) at two eddy covariance (EC) sites in alkaline desert ecosystems over Central Asia. Simulations of the net radiation (R-net), latent heat flux (Q(le)), sensible heat flux (Q(h)), and soil temperature showed that refined estimate of roughness length (Z(0m)) significantly improved the performance of CoLM in simulating turbulent heat fluxes Q(le) was increased but Q(h) was decreased, which were in better agreement with the observations from EC system. The results indicated that accurate parameterization of Z(0m) is of crucial importance for predicting energy and water fluxes in LSM when applied in Central Asia desert ecosystems. Sensitivity analysis regarding leaf area index (LAI), Z(0m), and albedo (alpha) showed that Rnet is very sensitive to alpha but Q(le), Q(h), and soil temperature (T-soil) are sensitively varying with the estimate of Z(0m) at the two EC sites over Central Asia.