Thermal boundary resistance (TBR) in semiconductor-on-diamond structure bottlenecks efficient heat dissipation in electronic devices. In this study, to reduce the TBR between GaN and diamond, surface-activated bonding with a hybrid SiOx-Ar ion source was initially applied to achieve an ultrathin interfacial layer. The simultaneous surface activation and slow deposition of the SiOx binder layer enabled precise control over layer thickness (2.5–5.3 nm) and formation of an amorphous heterogeneous nanostructure comprising a SiOx region between two inter-diffusion regions. Crucially, the 2.5-nm-thick interfacial layer achieved a TBR of 8.3 m2⋅K/GW, a record low for direct-bonded GaN/diamond interface. A remarkable feature is that the TBR is extremely sensitive to the interfacial thickness; Varying from 8.3 m2⋅K/GW to 34 m2⋅K/GW with thickness difference of only 2.8 nm. Theoretical analysis revealed the origin of this phenomena: a diamond/SiOx inter-diffusion layer extend the vibrational frequency, far exceeding that of crystalline diamond, which increases the lattice vibrational mismatch and suppresses phonon transmission.