Non-uniform thermal distribution affects about large periphery GaN HEMT based on through-via structure is analyzed in the paper. According to the self-heating effect and heat dissipation issues of Si-based GaN HEMT RF power devices, a high density through-via technology employing by conducting thermal near junction of multi-gate finger device downward to the heat sink is further put forward. Its corresponding placement provide a novel path for spreading heat directly from the heat source region of each of cell to the low temperature heat sink. From the thermal simulation with a total gate width of 8.1 mm, it is shown that compared with traditional structure devices, the maximum junction temperature of a uniform gate device with through-via structure is reduced by 34 °C, and the thermal resistance is reduced by 1.05 °C /W. Therefore, the through via technology as key process can play an important role in developing the large periphery RF GaN HEMT on high resistance Si substrate.