Multi-scale design in metal–support interaction allows for the comprehensive control of the electronic migration and magnetic respond behaviors, providing tuning frequency electromagnetic (EM) absorption. Herein, synergizing confined reduction and Kirkendall diffusion were proposed to design the metal Nickel (e.g. signal atoms, clusters and nanoparticles) in the carbon matrix. In our work, residual carbon (RC) was used as substrate to load carbon-encapsulated Ni particles to build unique magnetic–dielectric RC-Ni@C composites. With tuning multi-scale magnetic and electric interaction, as-synthesized RC-Ni@C composite exhibited remarkable tuning frequency absorption feature, which the RC-Ni@C-2 sample hold the outstanding EM dissipation in the low-frequency C-band (4–8 GHz). To confirm the magnetic and electric interaction, visual evidence of electric field distribution was offered via the advanced integrated differential phase contrast (iDPC) technology. Combined with density functional theory (DFT) calculation and EM parameters analysis, related EM energy absorption mechanisms were discussed in this multi-scale heterostructures, including the dielectric polarization, conduction loss and magnetic dissipation. As results, special gradient magnetic particles regulating in carbon substrates provide new design idea to build low-frequency EM wave absorption.