With the trend toward high-power radio-frequency (RF) electronic devices, flexible thermally conductive composite films are regarded as a key engineering interfacial material to address the critical problem of signal transmission and heat dissipation. However, achieving simultaneous optimization of high thermal conductivity and low loss in the same material remains a significant challenge, particularly in films with high filler loading. Here, a bottom-up regulatory strategy is proposed to address this challenge. Through the synergistic optimization of interface modification design and spatial orientation arrangement of hexagonal boron nitride (BN), the fabricated composite film achieves an exceptional in-plane thermal conductivity of 78.50 W m⁻1 K⁻1, significantly surpassing that of the film with BN. This remarkable enhancement is primarily attributed to the altered surface properties of the aminated BN (BN-NH2). The introduction of amine groups enhances the compatibility with the polymer matrix through electrostatic interactions to facilitate more efficient interfacial thermal transport. Furthermore, the highly oriented spatial arrangement of BN in the film not only preserves the electromagnetic wave transparency (99.94%), but also enhances its breakdown strength. This study underscores the critical role of molecular-level filler modification combined with micro-nanostructural engineering in synergistically strengthening the filler-matrix interface and boosting film thermal transport.