Abstract Thermal transport across GaN/c-BN heterostructures is investigated using molecular dynamics simulations with a neuroevolution potential (NEP). The influence of crystallographic orientation—(100), (110), and (111)—and interfacial atomic termination on the thermal boundary resistance (TBR) is systematically analyzed. At 300 K, the calculated TBR ranges from 2.23 to 3.10 m 2 ·K·GW -1 . Interfacial termination is found to exert a stronger influence than crystallographic orientation. In particular, N-B termination reduces the TBR by approximately 33% relative to Ga-N termination. This reduction correlates with a substantially larger vibrational density of states (VDOS) overlap (0.2872 for N-B compared to 0.0742 for Ga-N), consistent with improved phonon spectral matching arising from closer atomic mass similarity. Over the temperature range 200-600 K, the TBR decreases approximately linearly with increasing temperature, accompanied by a 9.33% increase in VDOS overlap and enhanced phonon participation rates. These results clarify the role of interfacial bonding and phonon spectral coupling in governing thermal transport across GaN/c-BN interfaces.