Wide and ultrawide bandgap semiconductors, such as GaN, play a crucial role in high-power applications, yet their performance is often constrained by thermal management challenges. In this work, we introduce a high-quality interface between GaN and AlN, prepared through wafer-scale bonding and verified via high-resolution transmission electron microscopy and transport experiments. We experimentally measured the thermal boundary conductance of the GaN–AlN interface, achieving up to 320 MW/m2K at room temperature using an ultrafast optical technique and sensitivity examinations. Non-equilibrium atomistic Green's functions and density functional theory simulations were conducted to model the interface phonon modes and their contributions to thermal transport, demonstrating good agreement with the experimental results from 80 to 300 K. Additionally, we observed a size-dependent effect on the thermal boundary conductance related to the GaN film thickness from 180 to 450 nm, which we attributed to quasi-ballistic thermal transport through molecular dynamics simulations. Our study has demonstrated a scalable processing route for wafer-sized chip packaging and provides fundamental insights to mitigate near-junction thermal resistance. Further exploration of interface engineering could facilitate co-design strategies to advanced thermal management technologies.