High-density 3D thermally conductive nanofiller network plays a vital role in the fabrication of polymer-based composites with high thermal conductivity (TC) for thermal management systems. In this work, highly thermally conductive polystyrene (PS)-based composites were prepared by introducing boron nitride nanosheets-coated melamine foam (MF@BNNSs) and carboxylated multi-walled carbon nanotubes (MWCNT–COOH). In this unique structure, MF@BNNSs can provide a 3D thermally conductive network, while MWCNT–COOH is embedded into the MF@BNNSs skeleton to improve the network-density. Specifically, the TC of PS/MWCNT/MF@BNNSs composite with 0.6 wt% MWCNT–COOH loading reaches 5.33 W /m· K, about 4.4-fold as high as that of the PS/MF@BNNSs. Moreover, the PS/MWCNT/MF@BNNSs composite exhibits effective heat dissipation capacity after assembling the power LED chip. Due to the isolation effect of MF@BNNSs skeleton, the PS/MWCNT/MF@BNNSs maintain electrical insulation properties. Consequently, the design of the thermal conductive network based on MF@BNNSs and MWCNT–COOH offered a substantial potential avenue for the preparation of polymer-based composites with high TC and insulating properties.