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[Display omitted] • We study the ITRs of AlN/graphene/SiC heterostructures by molecular dynamics simulation. • The ITRs decrease with the increase of the numbers when the height of the NNFSs is lower than the cutoff distance. • The ITRs increase significantly when the height of the NNFSs is higher than the cutoff distance of the interaction. • The change of the ITRs arises from the combined effect of sub-interfacial interactions and the overlaps of PDOS. Revealing the heat transport mechanism in typical heterostructures is crucial for designing GaN power chips with better engineering heat transfer performance. Herein, the effect of nanoscale nonplanar feature structures (NNFSs) on the interfacial thermal resistances (ITRs) of w-AlN/bilayer graphene/3C-SiC heterostructures is investigated systematically by molecular dynamics. The results indicate that the increase of the NNFSs numbers contributes to the decrease of the ITRs when the height is lower than the cutoff distance of the interaction. Multiple analyses indicate that, although the interactions at two van der Waals sub-interfaces (w-AlN/graphene and graphene/graphene) slightly weaken the phonon transfer, the increase of the NNFSs numbers enlarge the overlaps of phonon density of state (PDOS), which provides more phonon transfer channels. However, when the height is higher than the cutoff distance, the ITRs increase significantly due to the double decrease of the interactions and the overlaps of PDOS for the w-AlN/graphene sub-interface. These phenomena are further verified by the transient transport of energy. Besides, the NNFSs with random distribution also contribute to the reduction of the ITRs. We believe that the results of this work will provide significant guidance for improving the thermal transport performance of GaN power chips. [ABSTRACT FROM AUTHOR]