Rational design on the microstructure of microwave-absorbing materials is paving the way for upgrading their performances in electromagnetic pollution prevention. In this study, a Fe3O4/C composite with unique yolk-shell microstructure (YS-Fe3O4@C) is successfully fabricated by a silica-assisted route. It is found that carbon shells in this composite can make up the shortages of Fe3O4 microspheres in dielectric loss ability, while they may more or less attenuate the intrinsically magnetic loss of Fe3O4 microspheres. The microwave absorption properties of YS-Fe3O4@C are evaluated in the frequency range of 2.0-18.0 GHz in terms of the measured complex permittivity and complex permeability. The results demonstrate that YS-Fe3O4@C can exhibit much better performance than bare Fe3O4 microspheres and individual carbon materials, as well as core-shell Fe3O4/C composite (CS-Fe3O4@C), where strong reflection loss and wide response bandwidth can be achieved simultaneously. With an absorber thickness of 2.0 mm, the maximum reflection loss is -73.1 dB at 14.6 GHz and a bandwidth over -10.0 dB is in the range of 12.3-18.0 GHz. It can be proved that the unique yolk-shell microstructure is helpful to reinforce the dielectric loss ability and create an optimized matching of characteristic impedance in the composite.