This work reports the preparation of graphene nanoplatelet (GNP)/multiwalled carbon nanotube (MWCNT)/ polypyrrole (PPy) hybrid fillers via in situ chemical oxidative polymerization with the addition of a cationic surfactant, hexadecyltrimethylammonium bromide. These hybrid fillers were incorporated into polyurethane (PU) to prepare GNP/MWCNT/PPy/PU nanohybrids. The electrical conductivity of the nanohybrids was synergistically enhanced by the high conductivity of the hybrid fillers. Furthermore, the electromagnetic interference (EMI) shielding effectiveness (SE) was greatly increased by interfacial polarization between the GNPs, MWCNTs, PPy, and PU. The optimal formulation for the preparation of GNP/MWCNT/PPy three-dimensional (3D) nanostructures was determined by optimization experiments. Using this formulation, we successfully prepared GNP/PPy nanolayers (two-dimensional) that are extensively covered by MWCNT/PPy nanowires (one-dimensional), which interconnect to form GNP/MWCNT/PPy 3D nanostructures. When incorporated into a PU matrix to form a nanohybrid, these 3D nanostructures form a continuous network of conductive GNP−PPy−CNT−PPy−GNP paths. The EMI SE of the nanohybrid is 35−40 dB at 30−1800 MHz, which is sufficient to shield over 99.9% of electromagnetic waves. Therefore, this EMI shielding material has excellent prospects for commercial use. In summary, a nanohybrid with excellent EMI SE performance was prepared using a facile and scalable method and was shown to have great commercial potential.