Abstract The regulation of heteroatoms and heterogeneous interface characteristics has emerged as a promising strategy to enhance electromagnetic wave (EMW) absorption. However, challenges remain in precisely controlling heteroatom doping and fully understanding the synergistic mechanisms between heteroatoms and heterogeneous interfaces. Here, a novel strategy is proposed for enhancing synergistic polarization relaxation through heteroatom optimization. Carbon nanofiber (CNF)‐based Ni–Fe nanocubes decorated with N and O heteroatoms are synthesized by pyrolyzing Fe‐based metal–organic frameworks under different atmospheres (NH 3 , H 2 /Ar, Ar). The results show that N, O heteroatoms play a crucial role in the synergistic polarization effect by regulating the electronic structure and diverse heterogeneous structures. Finally, Fe 2 N@Ni 3 Fe/CNFs exhibit excellent EMW absorption at 2.3 mm, with a minimum reflection loss of −56.75 dB, and an effective absorption bandwidth of 6.7 GHz. Additionally, these materials display remarkable corrosion resistance due to their unique fiber network structure. This study highlights the role of heteroatoms in optimizing synergistic polarization effects, offering valuable insights for the design of advanced EMW absorption materials with heteroatom‐optimized heterointerfaces.