Green electromagnetic interference (EMI) shielding materials have been popularly accepted as the most promising EMI shielding material used in the electronic industrial community. Nevertheless, the design and optimization for both material and structure to achieve this function remain many challenges. Herein, Fe 3 O 4 @PA6 microspheres were fabricated by an unusual reaction-induced phase separation method, where Fe 3 O 4 nanoparticles were in situ introduced into the polymerization system. Interestingly, most Fe 3 O 4 nanoparticles spontaneously immigrated into PA6 microsphere, forming Fe 3 O 4 @PA6 composite microspheres, and more interestingly, the saturation magnetization and particle size of the microspheres are highly associated. Therefore, the microspheres with specific particle size and magnetic property were easily obtained by simple sieving. These microspheres were then coated by MWCNT and hot-compressed into EMI materials with segregated structures. A multilayered structure with positive conductivity gradients and negative magnetic gradients were created. Due to this structure, electromagnetic wave can enter the materials from the impedance matching channel without a large amount of reflection on the surface. The results show that with the increase in the number of composite layers, the EMI SE increases to 24.8 dB, and the R-value is significantly reduced to 0.51. This work provides a new feasible idea for designing low-reflection EMI composites.