In this paper, the coupled WRF/SSiB model, accompanied by a Karst Rocky Desertification (KRD) map of the Guizhou Karst Plateau (GKP) of China, was applied to detect how the changed vegetation and soil characteristics over the GKP modify the energy balance at the land surface. The results indicated that land degradation led to reduced net radiation by inducing more upward shortwave and longwave radiation, which were associated with increasing surface albedo and temperature, respectively. The KRD also resulted in changed surface energy partitioning into sensible and latent heat fluxes. The latent heat flux at land surface was reduced substantially due to the higher surface albedo and stomatal resistance, the lower Leaf Area Index (LAI) and roughness length in the degradation experiment, while the sensible heat flux increased, mainly because of the higher surface temperature. Furthermore, the moisture flux convergence was reduced, owing to the lower atmospheric heating and the relative subsidence. However, compared with the reduced evaporation, the decrease in moisture flux convergence contributed much less to the reduced precipitation. Precipitation strongly affects soil moisture, vegetation growth and phenology, and thus evaporation and convective latent heating, so when precipitation was changed, a feedback loop was created.