Thermally conductive polymeric materials with versatility are in high demand in electronic devices. Whereas, the limited thermal conductivity (TC) and versatility restrict the development of such materials. Herein, the hierarchical design and assembly technology was applied to prepare multifunctional functionalized boron nitride/polyurethane multi-layer (m-FBN/PU) fibrous membranes with higher quality and higher quantity of thermally conductive network. Filler layers act as thermally conductive pathways and substrate layers provide mechanical support and the obtained hydrophobic and flexible m-FBN/PU fibrous membranes with 10 wt% FBN filling display high TC (5.78 W·m−1·K−1) and electrical insulation (1014 Ω·cm). Meanwhile, in comparison with the FBN/PU single-layer fibrous membranes, the thermal conductive enhancement reaches 61.5 %, which could be ascribed to the increased phonon transfer network built by the alternated aligned hierarchical structure. Our fabrication provides a promising strategy for developing multifunctional polymeric materials and has the potential in advanced electronics and emerging fields like wearable electronics.