With the gradual miniaturization and integration of electronic devices, the design and development of new high thermal conductivity polymer-based composite materials are crucial for enhancing the performance of modern electronic devices. In this study, three-dimensional boron nitride (3D-BN) aerogels with vertically aligned structures were prepared using the ice templating method, serving as the primary thermal conductive network. Subsequently, aluminum oxide (Al2O3)/epoxy resin (EP) nanofluids were infiltrated into the aerogel’s air pores using vacuum impregnation. The Al2O3 particles in contact with each other formed the secondary thermal conductive network. Thus, a 3D BN-Al2O3/EP composite material with a dual thermal conductive network structure was successfully fabricated. The composite material exhibited a high thermal conductivity coefficient of 1.077 Wm−1K−1 when loaded with 17.67 wt% BN and 26.23 wt% Al2O3, representing a 496 % increase compared to pure EP and a 211 % increase compared to 3D-BN/EP composite materials. Furthermore, this composite material demonstrated excellent thermal stability and mechanical properties. This work provides a new direction for designing novel polymer-based composite materials with low filler loading and high thermal conductivity performance.