Well-ordered core/shell/shell-like Fe3O4@SiO2@PPy microspheres with prominent electromagnetic microwave absorption performance were successfully obtained by microemulsion polymerization method. The morphology, crystal form, functional group, magnetism and microwave absorption properties were investigated. The tailored shell thickness can be tuned from 20 to 60 nm (including SiO2 layer) via changing the molar ratio of Fe3O4@SiO2 to Pyrrole. The absorption peak positions gradually move to low frequency with increment of coating thicknesses. The minimum RL reached −40.9 dB at 6 GHz with the coating thickness of 5 mm. The effective absorption bandwidth could reach 6.88 GHz from 11.12 to 18 GHz, completely covering the whole K (12–18 GHz) band. Meanwhile, it showed excellent wave absorption in 4.4–18 GHz with different coating thickness. The perfect electromagnetic wave absorption properties could be attributed to the dielectric loss from the special core/shell/shell microstructure and natural resonance from the Fe3O4 microspheres. These newly prepared Fe3O4@SiO2@PPy microspheres might be considered as prospective nominees for highly efficient microwave absorption materials with tailored nanostructures.