To examine the differences of thermal characteristics introduced by material thermal conductivity, anisotropic polycrystalline diamond (PCD) and GaN are analyzed based on the accurate model of grain sizes in the directions of parallel and vertical to the interface and an approximate solution of the phonon Boltzmann transport equation. Due to the space-variant grain structures of PCD, the inhomogeneous-anisotropic local thermal conductivity, homogeneous-anisotropic thermal conductivity averaged over the whole layer and the typical values of inhomogeneous-isotropic thermal conductivity are compared with/without anisotropic GaN thermal conductivity. The results show that the considerations of inhomogeneous-anisotropic PCD thermal conductivity and anisotropic GaN thermal conductivity are necessary for the accurate prediction of temperature rise in the GaN HEMT devices, and when ignoring both, the maximum temperature rise is undervalued by over 16 K for thermal boundary resistance (TBR) of 6.5 to 60 m2K/GW at power dissipation of 10 W/mm. Then the dependences of channel temperature on several parameters are discussed and the relations of thermal resistance with power dissipation are extracted at different base temperature. Compared with GaN, SiC and Si substrates, PCD is the most effective heat spreading layer though limited by the grain size at initial growth interface.