Crop growth and agricultural management can affect climate at various spatial and temporal scales through the exchange of heat, water, and gases between land and atmosphere. Therefore, simulation of fluxes for heat, water, and gases from agricultural land is important for climate simulations. A land surface model (LSM) combined with a crop growth model (CGM), called an LSM-CGM combined model, is a useful tool for simulating these fluxes from agricultural land. Therefore, we developed a new LSM-CGM combined model for paddy rice fields, the MATCRO-Rice model. The main objective of this paper is to present the full description of MATCRO-Rice. The most important feature of MATCRO-Rice is that it can consistently simulate latent and sensible heat fluxes, net carbon uptake by crop, and crop yield by exchanging variables between the LSM and CGM. This feature enables us to apply the model to a wide range of integrated issues.