GaN-based HEMTs have the potential to be widely used in high-power and high-frequency electronics while their maximum output powers are limited by high channel temperature induced by near-junction Joule-heating, which degrades device performance and reliability. Increasing the TBC between GaN and SiC will aid in the heat dissipation of GaN-on-SiC power devices, taking advantage of the high thermal conductivity of the SiC substrate. However, a good understanding of the TBC of this technically important interface is still lacking due to the complicated nature of interfacial heat transport. In this work, a lattice-mismatch-insensitive surface activated bonding method is used to bond GaN directly to SiC and thus eliminating the AlN layer altogether. This allows for the direct integration of high quality GaN layers with SiC to create a high thermal boundary conductance interface. TDTR is used to measure the thermal properties of the GaN thermal conductivity and GaN-SiC TBC. The measured GaN thermal conductivity is larger than that of GaN grown by MBE on SiC, showing the impact of reducing the dislocations in the GaN near the interface. High GaN-SiC TBC is observed for the bonded GaN-SiC interfaces, especially for the annealed interface whose TBC (230 MW/m2-K) is close to the highest values ever reported. To understand the structure-thermal property relation, STEM and EELS are used to characterize the interface structure. The results show that, for the as-bonded sample, there exists an amorphous layer near the interface for the as bonded samples. This amorphous layer is crystallized upon annealing, leading to the high TBC found in our work. Our work paves the way for thermal transport across bonded interfaces, which will impact real-world applications of semiconductor integration and packaging.