Nanofiller reinforced carbon-matrix nanocomposites (Nanofiller/Cs) have great potential for aerospace military applications, owing to their lightweight, high specific strength and capable of shielding electromagnetic interference (EMI) at extreme temperature conditions. Motivated by this, many researchers focus on infiltrating pyrocarbon into carbon nanotube (CNT) assemblies to fabricate CNT/Cs. Despite attractive results, Nanofiller/Cs with combination of excellent mechanical and EMI shielding properties have not been realized so far. Herein, a 3D core-shell nanofiller of [email protected] ([email protected]) is incorporated into pyrocarbon system to fabricate novel cellular [email protected]/Cs. The core-shell [email protected] induces notably crack-tip blunting and crack deflection during fracture, giving [email protected]/Cs significantly increased mechanical properties at optimized G layers: 43.2% in flexural strength and 102.7% in fracture toughness, compared to the porous neat carbon. Moreover, introduction of [email protected] enhances EMI shielding effectiveness (SE) in X-band from 26.6 to 45.3 dB, resulting in high specific SE of 43.1 dB cm3/g with ultralow density of 1.05 g/cm3. The excellent shielding capability mainly stems from remarkably enhanced absorption loss caused by conductive G skeleton, special G-CNT junction interfaces and unique cellular structures. This work provides a promising methodology to prepare ultralight high-performance Nanofiller/Cs by combining reinforcement and functionality of [email protected] and toughening effect of core-shell structures.