Transport mechanisms, such as mass and heat transfer, are critical to the efficiency and the reliability of nuclear fuels such as uranium oxide. These properties can be significantly affected by the microstructure of the material. This paper looks into the effects of grain boundary (GB) Kapitza resistance on the overall heat conductivity of UO2 using a 3-D finite element model with microstructurally explicit information. The model developed is created with a 3-D reconstruction of the microstructure of depleted uranium samples performed using serial sectioning techniques with Focused Ion Beam (FIB) and Electron Backscattering Diffraction (EBSD). The model treats grain bulks, GBs and triple junctions using elements of different dimensionalities, and it is thus capable of incorporating information of all three entities in one model while keeping a manageable computational cost. Furthermore, the properties of these microstructural entities are characterized by misorientation angles and Coincident Site Lattice (CSL) models, which provide a framework to assign spatially dependent thermal and mass transfer properties based on the location and connectivity of these entities in actual microstructures. Coupling between heat transfer and mass transfer of fission products is also taken into account in the study, to make it a multi-physics model capable of following the evolution of thermal performance as fission products are produced. These simulations can provide input and insight into the fuel pellet behaviors at the initial stage of power generation when burnups are low.