In this study, the initial soil moisture in an atmospheric model was varied by assimilating AMSR-E (The Advanced Microwave Scanning Radiometer for EOS) products, and the results were compared with the default model scenario and in-situ data based on long-term CAMP/Tibet (Coordinated Enhanced Observing Period (CEOP) Asia-Australia Monsoon Project (CAMP) Tibet) observations. The differences between the obtained results (i.e., the new simulation, default model configuration and in-situ data) showed an apparent inconsistency in the model-simulated land surface heat fluxes. The results showed that the soil moisture was sensitive to the specific model simulation. To evaluate and verify the model stability, a long-term modeling study with AMSR-E soil moisture data assimilation was performed. Based on test simulations, AMSR-E data were assimilated into an atmospheric model for July and August 2007. The results showed that the land surface fluxes agreed well with both the in-situ data and the results of the default model configuration. Assimilating the AMSR-E SM products was important for determining the land surface heat fluxes in the WRF model. All the assimilation work substantially improved the modeling of land surface heat fluxes. Land surface heat fluxes are related to atmospheric interactions. Therefore, land surface heat fluxes are very important land surface parameters during these processes. Therefore, the simulation can be used to retrieve land surface heat fluxes from an atmospheric model. It is important to study the surface heating sources that are related to both the water and energy cycles over the Tibetan Plateau.