Carbon-based magnetic nanocomposites as promising lightweight electromagnetic wave (EMW) absorbents are expected to address critical issues caused by electromagnetic pollution. Herein, Fe3O4 nanoparticles embedded into a 3D N-rich porous carbon nanohoneycomb (Fe3O4@NC) were developed via the pyrolysis of an in-situ-polymerized compound of m-phenylenediamine initiated by FeCl2 in the presence of NaCl crystals as templates. Results demonstrate that Fe3O4@NC features highly dispersed Fe3O4 nanoparticles into an ultrahigh specific pyridinic-N doping carbon matrix, resulting in excellent impedance matching characteristics and electromagnetic wave absorbing capability with the biggest effective absorption bandwidth (EAB) of up to 7.1 GHz and the minimum reflective loss (RLmin) of up to -65.5 dB in the thin thickness of 2.5 and 2.3 mm, respectively, which also outperforms the majority of carbon-based absorbers reported. Meanwhile, its high absorption performance is further demonstrated by an ethylene propylene diene monomer wave absorbing patch filled with 8.0 wt % Fe3O4@NC, which can completely shield a 5G signal in a mobile phone. In addition, theory calculation reveals that there is a strongest dx2-Pz orbital hybridization interaction between Fe3O4 clusters and pyridinic-N dopants in the carbon network, compared with other kinds of N dopants, which can not only generate more dipoles of carbon networks but also increase net magnetic moments of Fe3O4, thereby leading to a coupling effect of efficient dielectric and magnetic losses. This work provides new insights into the precise design and synthesis of carbon-based magnetic composites with specific interface interactions and morphological effects for high-efficiency EMW absorption materials.