Accurate modeling of water, heat and carbon dioxide fluxes is of importance in understanding the energy and mass exchange processes between land surface and atmosphere. This paper focuses on the advance in processes-based water, heat and CO2 fluxes simulation model and reviews the development of statistic, integrated and remote sensing-based models for estimating water, heat and carbon dioxide fluxes in the soil-plant-atmosphere continuum. The reviewed statistic models included models that estimate water and heat fluxes based on temperature, humidity and radiation, and models that simulate carbon dioxide flux based on climatic factors, evapotranspiration and light use efficiency. Reviewed processes-based models covered the big-leaf model, two-source model, multi-source model and multi-layer models for water and heat transfer as well as leaf-level to canopy level models for carbon dioxide flux. Integrated models included biophysical, biochemical and biogeographic models. The statistic models are applied widely in directing the simulation of water, heat and CO2 fluxes at large-scale level because of simple form and because the required data are obtained easily. While the process-based models describe the physical and physiological processes of water, heat and CO2 flux transfer accurately and have been the foundation of large-scale integrated models. The future development of flux models is to integrate various method and technology for multi-scale network measuring and large-scale mechanism modeling.