We report the temperature dependent thermal properties of two types of GaN composite substrates (GaN-SiC and GaN-Si) using picosecond time-domain thermoreflectance (TDTR). The intrinsic thermal conductivity of the GaN buffer film decreases with increasing temperature, while the GaN-substrate thermal interface resistance (TIR) increases with increasing temperature. The strong temperature dependence of the GaN-substrate TIR suggests that microstructural defects within the AlN transition film and near its boundaries can be particularly important.