The high-performance electronic equipment appearing in the information age puts forward more comprehensive requirements for polymer-based composites with high heat dissipation capability, good mechanical properties, and substantial fire safety performance. However, the low interfacial interaction caused by the phase structural difference between the fillers greatly reduced the improvement of performance of the composites. It is feasible to overcome this issue by forming chemical interaction to regulate the interface structure. Herein, an anisotropic oriented composite is obtained by layer-by-layer self-assembly stacking of one-dimensional aramid nanofibers (ANFs) and ionic liquid (IL) functionalized two-dimensional boron nitride nanosheets (BNNSs). Considering the influence of the interface structure on the performance, the IL containing imidazolium ring and hexadecyl selected by density functional theory (DFT) form effective interface interactions with BNNSs. Owing to the establishment of multiple non-covalent bonding (cation–π, and CH–π) interactions, the composite exhibits not only high thermal conductivity (15.2 W m⁻¹ K⁻¹) and tensile strength (63.2 MPa) but also has excellent flame-retardant properties (limited oxygen index ≈ 45). Such an outstanding performance results in effectively cool light-emitting diode modules and desktop computers, outperforming a commercial thermal gasket. Significantly, molecular dynamics (MD) and DFT simulations further elucidate the role of IL in promoting heat transfer and the thermal conductivity mechanism between BNNS interfaces, respectively. This study offers a feasible strategy for constructing an interfacial structure by screening the modifier molecular configuration to perfect the excellent versatility of thermal management composites.