With the trend of device miniaturization and higher integration, polymer composites with high thermal conductivity are highly desirable for efficient removal of accumulated heat to maintain high performance of electronics. In this work, epoxy composites embedded with three-dimensional hexagonal boron nitride (BN) scaffold were fabricated. The BN-poly(vinylidene difluoride) (PVDF) scaffold was prepared by the salt template method using PVDF as the adhesive, while the corresponding epoxy composite was manufactured with vacuum-assisted impregnation. The epoxy/BN-PVDF composite exhibits high thermal conductivity with low loading of BN. The thermal conductivity of epoxy/BN-PVDF composite achieved 1.227 W/(m K) with 21 wt % BN, contributed by the constructed BN pathway held together by PVDF adhesive. In addition, PVDF could be further converted into carbon by thermal treatment, further enhancing the thermal conductivity of epoxy/BN-C composites through alleviating the phonon scattering at the interfaces, eventually obtaining thermal conductivity of 1.466 W/(m K). This type of epoxy-based composite with high thermal conductivity is promising to be used as thermal management materials in advanced electronic devices.