As one of the emerging nanomaterials, boron nitride nanotubes (BNNTs) provide promising opportunities for diverse applications due to their unique properties, such as high thermal conductivity, immense inertness, and high-temperature durability, while the instability of BNNTs due to their high surface induces agglomerates susceptible to the loss of their advantages. Therefore, the proper functionalization of BNNTs is crucial to highlight their fundamental characteristics. Herein, a simplistic low-cost approach of BNNT surface modification through catechol-polyamine (CAPA) interfacial polymerization is postulated to improve its dispersibility on the polymeric matrix. The modified BNNT was assimilated as a filler additive with AlN/Al2O3 filling materials in a PDMS polymeric matrix to prepare a thermal interface material (TIM). The resulting composite exhibits a heightened isotropic thermal conductivity of 8.10 W/mK, which is a ~47.27% increase compared to pristine composite 5.50 W/mK, and this can be ascribed to the improved BNNT dispersion forming interconnected phonon pathways and the thermal interface resistance reduction due to its augmented compatibility with the polymeric matrix. Moreover, the fabricated composite manifests a fire resistance improvement of ~10% in LOI relative to the neat composite sample, which can be correlated to the thermal stability shift in the TGA and DTA data. An enhancement in thermal permanence is stipulated due to a melting point (Tm) shift of ∼38.5 °C upon the integration of BNNT-CAPA. This improvement can be associated with the good distribution and adhesion of BNNT-CAPA in the polymeric matrix, integrated with its inherent thermal stability, good charring capability, and free radical scavenging effect due to the presence of CAPA on its surface. This study offers new insights into BNNT utilization and its corresponding incorporation into the polymeric matrix, which provides a prospective direction in the preparation of multifunctional materials for electric devices.