Phonon heat transfer across a vacuum nanogap can be induced by quasi-Casimir coupling without electromagnetic fields. For the thermal energy transport of diatomic molecules, the contribution of the atomic surface termination to the phonon heat transfer across a solid–vacuum–solid nanogap is still not well understood. Here, we investigated the thermal energy transport across a SiC–SiC nanogap with four kinds of atomic surface terminations using classical non-equilibrium molecular dynamics simulations. The thermal resonance between interfacial layers of identical atomic termination results in significant heat transfer enhancement across the SiC–SiC nanogap, while that of non-identical atomic termination is unnoticeable.