Abstract: Optimizing polymeric material properties through composite filler incorporation has demonstrated effectiveness in enhancing both thermal conductivity and electromagnetic wave absorption. However, persistent challenges arise from filler incompatibility and the intrinsic trade-off between thermal conductivity and electromagnetic wave absorption performance. This study develops a facile fabrication method for epoxy-based composites containing boron nitride-coated multi-walled carbon nanotube (BN/MWCNT) composite fillers, designed for dual thermal management and electromagnetic wave absorption applications. By controlling the BN coating extent on MWCNT surfaces, we facilitated precise regulation of dielectric properties and microstructural characteristics. Subsequent surfactant modification strengthened interfacial adhesion between fillers and matrix while suppressing particle agglomeration. The engineered coating architecture simultaneously reduced interfacial thermal resistance and established optimized conductive pathways. The composite achieved over 99% absorption across the entire X-band at 5wt% filler loading, with a minimum reflection loss of −39 dB. Concurrently, the thermal conductivity showed an increase of 104% compared to neat epoxy resin, confirming effective thermal network formation. This work establishes a practical approach for creating multifunctional electronic packaging composites through rational filler compounding and interface engineering.