Design optimization of an encapsulated carbon composite thermal control (TC) system is presented. The composite TC system consists of multiple phase change materials (PCM) doped with carbon nanotubes and enclosed in a casing of carbon/carbon composite sheets. Using the concept of global thermal resistance an analytical model was formulated to predict the transient temperature distribution through the composite system. The temperature data was then used to estimate maximum energy storage and heat dissipation rates. A substantial reduction in weight and size of the TC composite was observed corresponding to the optimized design. The use of carbon nanotubes both as additives with optimal loading and as a thermal interface material significantly reduced the maximum junction temperatures for different constant power loads for the multiple PCM composite as compared to its original size used for the experimental work. The optimized composite minimized the total thermal resistance through the composite sample and thereby increased its thermal response as indicated by approximately 4 times increase in the heat dissipation rate.