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 oC, 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. After bonding, the 15 nm Si interlayer achieved a higher TBC. The post-annealing significantly increased the TBC of both interfaces, while the TBC of 22 nm silicon interlayer increased greater and became higher than that of 15 nm. Detailed investigation of the microstructure and composition of the interfaces were carried out to understand the difference in interfacial thermal conduction. The obtained stress was no more than 230 MPa for both before and after the annealing, and this high thermal stability of the bonded composites indicates that the room temperature bonding can realize a GaN-on-diamond template suitable for further epitaxial growth or device process. This work brings a novel strategy of SAB followed by high-temperature annealing to fabricate a GaN-on-diamond device with a high TBC.