Owing to the excellent thermal properties of graphene, silicon carbide (SiC) combined with graphene is expected to obtain more outstanding thermal performance and structural stability at high temperatures. Herein, the thermal conductivity of graphene/SiC heterostructures (GS-Hs) with different structures and atomic orientations was calculated through non-equilibrium molecular dynamics (NEMD) simulations. The temperature dependence and size effect on the thermal transport properties of GS-Hs were systematically investigated and discussed. The continuous addition of graphene layers did not always have a positive effect. The thermal transport performance of GS-Hs approached the intrinsic thermal conductivity of SiC when the interaction gradually decreased with the distance between SiC and graphene. Studies on temperature and size dependence show opposite trends. The enhancement effect of graphene was limited at small distances. The thermal conductivity of GS-Hs had a negative correlation with temperature and increased with the system size. Meanwhile, the thermal conductivity of GS-Hs was predicted to be 156.25 (W·m⁻¹·K⁻¹) at the macroscopic scale via extrapolation. The model established in this paper is also applicable to other material simulation processes, as long as the corresponding parameters and potential functions are available. This study will provide inspiration for the optimized design and preparation of highly efficient cladding materials in nuclear reactors.