Thermal conductivity is one of the most significant criterion of three-dimensional carbon fiber-reinforced SiC matrix composites (3D C/SiC). Represent volume element (RVE) models of microscale, void/matrix and mesoscale proposed in this work are used to simulate the thermal conductivity behaviors of the 3D C/SiC composites. An entirely new process is introduced to weave the preform with three-dimensional orthogonal architecture. The 3D steady-state analysis step is created for assessing the thermal conductivity behaviors of the composites by applying periodic temperature boundary conditions. Three RVE models of cuboid, hexagonal and fiber random distribution are respectively developed to comparatively study the influence of fiber package pattern on the thermal conductivities at the microscale. Besides, the effect of void morphology on the thermal conductivity of the matrix is analyzed by the void/matrix models. The prediction results at the mesoscale correspond closely to the experimental values. The effect of the porosities and fiber volume fractions on the thermal conductivities is also taken into consideration. The multi-scale models mentioned in this paper can be used to predict the thermal conductivity behaviors of other composites with complex structures.