In order to regulate thermal transfer characteristics of graphene/silicon carbide heterogeneous interface, the influence of temperature, size and material defect rate on thermal conductance of heterogeneous interface are studied by the non-equilibrium molecular dynamics method. The sandwich model of graphene/silicon carbide heterostructures with different lengths and thickness is built by Material Studio. The reasons for the change of thermal conductance are analyzed from the two aspects of phonon density of states and phonon participation rate. When the system temperature is below the Debye temperature of silicon carbide and graphene, the quantum corrections is used to calculate the thermal conductance of heterostructure in the paper. The results show that the thermal conductance increases with the increase of temperature under both interfacial forces, but the thermal conductance of heterogeneous interface under covalent bond is higher than under van der Waals force. The main reason is that the density of states of graphene in a range of 10—30 THz increases significantly with the increase of temperature. The thermal conductance of heterogeneous interface decreases with the increase of silicon carbide layers, and decreases by 30.5% when the number of silicon carbide layers increases from 10 to 20. The thermal conductance of heterostructure is the lowest in the thermal conductances of 4 layers, it is considered that more phonons are transferred from local to delocalized mode in the middle and low frequency band. The introduction of vacancy defects can effectively improve the interface thermal conductance. At different temperatures, the interfacial thermal conductance first increases and then decreases with the increase of graphene defects, and the defect rate when the interfacial thermal conductance reaches the maximum value and the degree of interfacial thermal conductance decrease after reaching the maximum value is related to temperature. When the defect rate of silicon carbide and graphene are 20% and 35% respectively at 300 K, the interface thermal conductance reaches a maximum value. When the temperature is 900 K, the thermal conductance of graphene/silicon carbide heterogeneous interface reaches a maximum value when the defect rate is 30%. It is considered that the introduction of defects will hinder the medium frequency phonons from realizing the heat transport. The results show that the size effect and vacancy defect can be utilized to modify the heterogeneous interface, which is beneficial to the design and thermal management of the third-generation semiconductor micro-nano devices.