Thermal management of multi-chip module high power LED (MCM-LED) packaging is one key technology to the development of the reliable MCM-LED. In this paper, referring to MCM technology applied in IC packaging, and aiming at high power flip chip GaN-based LED packaging, the thermal analysis of MCM-LED is studied. Firstly, both a 2x2 flip chip LED array that is mounted on a bracket and heat dissipation packaging structure with the performance parameters of related materials are designed. Secondly, based on principle of heat transfer, the thermal resistance network of MCM-LED heat dissipation system is expressed, and the thermal resistance of cooling channel is theoretically calculated. The total thermal resistance and the junction temperature of LED chip of theoretical value are about 6.53 KlW and 77.2°C respectively. Thirdly, based on numerical analysis method, a 3-D finite element model (FEM) is developed. The temperature distribution in the chips and packages are shown, and junction temperature and total thermal resistance of simulative value are 82.12°Cand 7.14 KlW respectively. Finally, by means of orthogonal design of experiments, the optimized prototype structure and its related parameters are concluded. Aiming at the related material and structure parameters of MCM-LED packaging, the diameter of bump is the most important factor to thermal performance, following by the bonding layer material, chip size, the thickness of bonding layer and chip spacing.