Human society’s need to build low-weight, high-strength and durable structures has increased the demand for composite materials. In this case, composites are used where high mechanical strength, low weight, sound and thermal insulation properties are required. One of the most important issues now is designing materials and coatings aimed at reducing heat loss and resisting high temperatures. One way to address this problem is to develop a technique for preparing and applying composite materials that slow down their heating applied to a surface. In this study, carbon nanotubes (CNTs) reinforced composites were fabricated using silicone molding to be applied to honeycomb sandwich structures. To determine the effect of CNTs on the thermal behavior of the sandwich panels, different weight percentages of this material (0.025, 0.05. 0.075 wt.%) were added to the epoxy resin. The results showed that the thermal stability of the epoxy composites was directly related to the increase in the percentage of CNTs as the CNT content increased to 0.075 wt.%, and the thermal degradation temperature of the epoxy composites increased by 14 °C. In addition, the energy absorption increased by 4.6% with an increase in CNTs up to 0.075 wt.%. Density measurements showed that the density of the nanocomposite samples increased by adding CNTs to pure epoxy resin. The actual densities of the samples reinforced with 0.025, 0.05, and 0.075 wt.% CNTs are 0.925, 0.926, and 0.927 of the theoretical density, respectively. Since the CNT dispersion uniformity in the epoxy matrix can significantly affect the properties of the composites, in this study, a new method of dispersing CNTs in the epoxy resin matrix resulted in higher thermal conductivity while using lower amounts of CNTs compared to other studies. The storage modulus of the epoxy matrix composites reinforced with 0.05 wt.% in this study was 25.9% and 6.9% higher than that from the previous study reinforced with 0.1 wt.% and 0.25 wt.% CNTs, respectively. Furthermore, the tanδ and loss modulus of the composite reinforced with 0.05 wt.% CNTs in this study were 52% and 54.5% higher than that from the previous study with 0.1 wt.% CNTs, respectively. This study provided an optimal approach for designers and engineers who want to effectively design their composite honeycomb sandwich structure with better thermal properties.