<p>Mesophase pitch-based carbon fibers (CFs) with ultrahigh axial thermal conductivity can significantly enhance through-plane heat transfer in thermal interface materials by vertical alignment, yet raise short-circuiting and electromagnetic interference (EMI) risks. Although incorporating insulating fillers or coating CFs can suppress electron migration, it often compromises thermal performance. Herein, we engineer multi-functionally trunk-branch hierarchical heterostructures to address above limitations. Vertically aligned trunk-like CF scaffolds ensure superior through-plane heat transfer. Branch-like boron nitride (BN) networks optimize impedance matching by enhancing electrical insulation and consequently improve electromagnetic wave (EMW) absorption. Meanwhile, in situ BN networks interconnect CF scaffolds, extending bidirectional thermally conductive and EMW propagation paths. At only 20.17 vol% filler, the composite exhibits a through-plane thermal conductivity of 57.96 W·m⁻¹·K⁻¹ (specific thermal conductivity enhancement of 1431.62 %·(vol%)⁻¹) and an in-plane thermal conductivity of 2.93 W·m⁻¹·K⁻¹, together with excellent electrical insulation and absorption-dominated EMI shielding, addressing the challenge of thermal-electrical-electromagnetic coupling for next-generation electronics.</p>