Abstract The utilization of diamond as substrate for GaN power devices is regarded as a promising heat dissipation measure. However, the bonding interface between diamond and GaN wafers is prone to defects and significant interfacial thermal resistance (ITR). This issue severely compromises the thermal performance of the devices. This paper focuses on the urgent problems that need to be solved in high electron mobility transistors manufacturing, and systematically studies the influence of micro random vacancy defects on the heat transfer performance of GaN/diamond interface using non-equilibrium molecular dynamics method. The intrinsic mechanism was analyzed through radial distribution function and phonon density of states at the micro scale. The results showed that the ITR decreases gradually with the increase of random vacancy defect density in GaN. When the defect concentration reached 12%, the ITR was 11.89 (m 2 K)/GW, a decrease of 69%. Similarly, the increase of random defects in diamond will also reduce ITR. When the concentration of vacancy defects in diamond increased from 0 to 12%, the ITR decreased from 20.12 (m 2 K)/GW to 13.05 (m 2 K)/GW, a decrease of 54%. The research provides a theoretical basis for the thermal design of GaN/diamond devices.