To achieve high device performance and high reliability for the gallium nitride (GaN)-based high electron mobility transistors (HEMTs), efficient heat dissipation is important but remains challenging. Enormous efforts have been made to transfer a GaN device layer onto a diamond substrate with a high thermal conductivity by bonding. In this work, two GaN-diamond bonded composites are prepared via modified surface activated bonding (SAB) at room temperature with silicon interlayers of different thicknesses (15 nm and 22 nm). Before and after post annealing process at 800 °C, thermal boundary conductance (TBC) across the bonded interface including the interlayer and the stress of GaN layer are investigated by time-domain thermoreflectance and Raman spectroscopy, respectively. In the case of as-bonded samples, TBC of the 15 nm Si interlayer (32.4 MW/m2-K) was higher than that of the 22 nm (28.0 MW/m2-K); but after annealing, TBC of the 15 nm Si interlayer (71.3 MW/m2-K) became lower than that of the 22 nm (85.9 MW/m2-K), because the annealing is especially effective for thicker interlayer to improved interfacial TBC. The obtained stress was less than 230 MPa for both before and after the annealing, and this high thermal stability indicates that the room-temperature bonding can realize a GaN-on-diamond template suitable for further epitaxial growth or device process.