In this paper, the thermal design and optimization of a high-power wireless charging system (WCS) is proposed. An integrated electromagnetic and thermal co-optimization is essential to design a high power-density WCS pad. This study presents the thermal analysis and the potential optimization scopes for a polyphase WCS pad. The coil and core causes most of the power losses of a WCS pad and causes thermal hotspot in the pad. In this paper, the thermally conductive epoxy is introduced to balance the effective volumetric loss density in the pad and mitigate the thermal hotspots in the coil and core. The proposed design is simulated through finite element analysis (FEA) and tested experimentally for a 50 kW three-phase WCS. Simulation and experimental results show that the conventional design has localized hotspots in the coil and core. The proposed thermal design mitigates the thermal hotspots without increasing the coil or core volume.