The electrical performance and the long-term reliability of GaN-based high electron mobility transistors (HEMTs) are greatly affected by the Joule self-heating effect under high power density operation condition. Measurement of the junction temperature and analysis of the thermal resistance of the constituent layers including the packaging material are critically important for thermal design and reliability assessment of GaN-based HEMTs. In this paper, Raman thermometry combined with the finite element thermal simulation is used to compare the junction temperature and the thermal resistance of a GaN HEMT mounted on a novel Cu/graphite composite flange with those of a conventional CuMo flanged device. The results show that the junction temperature of the Cu/graphite flanged device is 15% lower than that of the CuMo flanged device at a power dissipation of 1.43 W/mm, while the overall device thermal resistance is 18.7% lower in the Cu/graphite flanged device. In addition, the temperature distributions of each layer along the cross-plane direction are analyzed for the two devices; the thermal resistance ratio of the Cu/graphite flange is 40% of the overall device thermal resistance, while the CuMo flange account for 53% of the overall thermal resistance of the device. This proves the effectiveness and benefit of using the Cu/graphite composite material package of high thermal conductivity to improve the heat dissipation of GaN HEMTs. By tuning the mass fraction of the graphite, it is possible to further increase the thermal conductivity of the Cu/graphite composite flange and to further reduce the device thermal resistance. It is observed in the Raman thermal measurement that the highest thermal resistance after flanging is the interfacial thermal resistance between the GaN epitaxial layer and the SiC substrate (~50 m²·K/GW). For obtaining the better thermal characteristics of the GaN HEMT, it is crucial to reduce the GaN/SiC interfacial thermal resistance through interface engineering during the epitaxial growth. In the meantime, Raman thermometry combined with the finite element thermal simulation is demonstrated to be an effective method for implementing the thermal characterization of the GaN-based devices and the constituent material layers, and the principle and procedure of the method are described in detail in the paper.