Designing multihierarchical electromagnetic wave-absorbing composite with multiphase, multieffective, and multidimensional properties is an effective way to improve absorption performance. Metal–organic frameworks (MOFs) have a high metal content and a stable carbon framework. By adjusting the metal type, organic ligand type, and precursor ratio during the preparation process, MOF materials with different morphologies can be synthesized and transferred into multihierarchical electromagnetic wave-absorbing composites via in situ pyrolysis. Herein, based on the Kirkendall diffusion effect, an in situ anisotropic-oriented growth strategy was advanced during the pyrolysis of Prussian blue, and a new magnetic carbon composite (γ-Fe2O3 @N-rGO/MWCNT) was prepared. The composite has a multihierarchical structure consisting of pinecone-like nanoflowers and a porous carbon framework. The nanoflowers are core-shell structures with γ-Fe2O3 magnetic nanoparticles as cores and nitrogen-doped reduced graphene oxides as shells interspersed in a porous carbon framework that includes intertwined multiwalled carbon nanotubes and amorphous carbon. The minimum reflection loss (RLmin) of the samples can reach up to − 59.2 dB at 5.51 GHz. The in situ anisotropic-oriented growth strategy used in this work shows great promise for the preparation of a variety of multihierarchical structure nanocomposite electromagnetic wave-absorbing materials with abundant absorption effects.