The design of a composite hybrid thermal control (TC) system for the thermal protection of electronics against transient pulsed power heat loads was investigated. Three types of materials: paraffin wax, carbon nanotubes (CNTs), and C/C composites are used in a novel design configuration to produce the hybrid TC system design. The hybrid TC system is tested for three cases: (1) TC system without CNT additives and thermal interface material (TIM), (2) TC system with CNT additives, and (3) TC system with both CNT additives and TIM. For each case the samples were subjected to uniform power condition and two types of varying power conditions. The TC system corresponding to case-2 showed a reasonable decrease in heater and junction temperatures as compared to case-1. However, substantial drop in heater and junction temperatures was found for case-3 as compared to case-1 and case-2. The results demonstrated the importance of using CNTs as an additive in paraffin wax and as a TIM in improving the thermal performance of a TC unit for protection against pulsed heat loads in electronics.