Abstract: Taking the Mekong River Basin as a study area, agricultural drought in monthly scale was predict based on the typical index of soil moisture of root layer by regional climate model(RegCM3) forced by the output of ECHAM5/MPI-OM global atmosphere-ocean coupled model in current(1980-2009) and future(2010-2039) under SRES A1B scenario in this paper. Based on the theory of surface energy balance, the relationship and changing regularity was analyzed between the main influencing factors of agricultural drought (such as precipitation, evaporation, surface temperature) and atmosphere circulation, energy fluxes (such as sensible flux, latent heat flux, surface net flux) simulated by RegCM3. From the aspects of surface energy and moisture flux balance, the mechanism of agriculture drought in the Mekong River Basin was preliminarily identified. The results show that the trend of the precipitation decrease, surface temperature increase, evaporation increase, and soil moisture decrease of experimental zone in late spring (June) and autumn (October) may cause the agricultural drought occurrence in local region of Mekong River basin in future.