How to design the microstructure of polymer nanocomposites to significantly improve their electromagnetic interference shielding effectiveness (EMI SE) is still a great challenge. Herein, we developed a template method for fabricating the 3D porous graphene nanoplatelets/reduced graphene oxide foam/epoxy (GNPs/rGO/EP) nanocomposites, in which 3D rGO foam embedded with GNPs constructs a 3D electrical and thermal conductive network inner EP matrix. The 3D rGO framework resolves the agglomeration problem of GNPs that acts as an efficient bunch of channels for electrical transport and attenuate the entered electromagnetic wave. Benefiting from the 3D nanohybrid framework, the GNPs/rGO/EP nanocomposites containing 0.1 wt% rGO and 20.4 wt% GNPs exhibit the maximum EMI SE value of 51 dB at the X-band, almost 292% improvement relative to the rGO/EP nanocomposites (～13 dB) and 240% enhancement compared with the GNPs/EP nanocomposites without 3D microstructure (～15 dB), and also presents an excellent thermal conductivity of 1.56 W/mK and electrical conductivity up to 179.2 S/m. This work provides a new strategy for designing muti-functional epoxy nanocomposites for EMI shielding and efficient heat dissipation.