Adding nanofillers into epoxy resin matrices is a common method to achieve their multi-function. Boron nitride nanotubes (BNNTs) with one-dimensional nanostructures have attracted much attention because of their ultra-high thermal conductivity, wide energy level band gap, high aspect ratio and mechanical strength. Yet, the strong π-π non-covalent bonding and lip-lip interactions make BNNTs prone to agglomeration in the epoxy resin matrix. Moreover, the different physicochemical properties of BNNTs and epoxy resins as well as the chemical inertness of BNNTs surface lead to the lack of effective interfacial interaction between BNNTs and epoxy resin matrix. Therefore, the performance of the epoxy composite dielectric is not enhanced by simple blending solely, but will even have the opposite effect. To address the problems of BNNTs, in this study, the surface structure of BNNTs is constructed from the perspective of interface modulation by using sol-gel method to coat mesoporous silica (mSiO ₂) on BNNTs’ surface and further introducing silane coupling agent (KH560). The results indicate that the surface structure of BNNTs can optimize the level of interfacial interaction between BNNTs and epoxy resin matrix, which leads to stronger interfacial connection and elimination of internal pore phenomenon. The dielectric constant and loss of the composite dielectric prepared in this way are further reduced, reaching 4.1 and 0.005 respectively at power frequency, which is significantly lower than that of pure epoxy resin. At the same time, the mechanical toughness (3.01 MJ/m ³) and thermal conductivity (0.34 W/(m⋅K)) are greatly improved compared with the counterparts of pure epoxy resin. In addition, the unique nano-mesoporous structure of mSiO ₂endows the composite dielectric with a large number of deep traps, which effectively hinders the migration of electrons, thereby improving the electrical strength of the composite dielectric, and the breakdown field strength reaches 95.42 kV/mm. Furthermore, the interfacial mechanism of BNNTs’ surface structure on dielectric relaxation and trap distribution of composite dielectrics is systematically studied by Tanaka multinuclear model. The above results indicate that the good interfacial interaction between BNNTs and epoxy resin matrix is crucial in establishing the micro-interface structure and improving the macroscopic properties of composite dielectrics. This study presents a novel idea for the multifunctionalities of epoxy resin, and also provides some experimental data support for revealing the correlation among surface properties of nano-fillers, microstructure and macroscopic properties of composite dielectric.