High thermal conductive filler (hexagonal boron nitride and carbon nanotube) reinforced polymer composites have obtained a growing attention in the microelectronic industry for their good thermal conductivity but electrical insulating. In this work, a synergistic hybrid structure of two fillers with different dimensions had been designed and prepared by taking hexagonal born nitride (h-BN) platelets and ammine carbon nanotubes (CNT-NH2) into the flexible polymer matrix. Using cycloaliphatic epoxy resin (CER) as the polymer matrix, a serious of (a) h-BN/CER based, (b) hybrid filler h-BN@CNT-NH2/CER based, and (c) mixed filler CNT-NH2 and h-BN/CER based composites were prepared. In this structure, h-BN (and h-BN@CNT-NH2) platelets stacked along the horizontal direction under the assistance of gravity force and interactivity between the fillers. The orientation of the h-BN platelets was investigated by scanning electron microscope (SEM) of the cracked cross-section of the composite film and XRD measurement via calculating the orientation function (f). The CNT-NH2 was embedded within the network to improve the filler-filler contact or network-density. Due to the anisotropic properties of h-BN platelets and dispersion states of CNT-NH2, the composites with different structures presented different and special properties, including thermal/electrical conductivity properties, mechanical properties, and thermal decomposition properties. The analysis of structure and mechanism of thermal decomposition were then proposed to explain those interesting properties. The incorporation and dispersion states of CNT-NH2 in the composites played an important effect on the enhancement of the thermal conductivity properties both included in plane (similar to 1.76 W/m.K) and through-plane (similar to 1.09 W/m.K) thermal conductivity. Additionally, the good electrical insulating properties and mechanical properties of the composites provided a potential application in the thermal management areas. The solvent-free procedure was environment friendly, easy operation, and suitable for the practical application in large scale.