By controlling the pyrolysis temperature, core/shell/shell structured Fe/Fe5C2/carbon nanotube bundles (Fe/Fe5C2/CNTBs), Fe/Fe3C/helical carbon nanotubes (Fe/Fe3C/HCNTs) and Fe/Fe3C/chain-like carbon nanospheres (Fe/Fe3C/CCNSs) with high encapsulation efficiency could be selectively synthesized in large-scale by water-assisted chemical vapor deposition method. Water vapor was proved to play an important role in the growth process. Because of α-Fe nanoparticles tightly wrapped by two layers, the obtained core/shell/shell structured nanohybrids showed high stabilities and good magnetic properties. The minimum reflection loss values of the as-prepared nanohybrids reached approximately -15.0, -46.3 and -37.1 dB, respectively. The excellent microwave absorption properties of the as-prepared core/shell/shell structured nanohybrids were considered to the quarter-wavelength matching model. Moreover, the possible enhanced microwave absorption mechanism of the as-prepared Fe/Fe3C/HCNTs and Fe/Fe3C/CCNSs were discussed in details. Therefore, we proposed a simple, inexpensive and environment-benign strategy for the synthesis of core/shell/shell structured carbon-based nanohybrids, exhibiting a promising prospect as high performance microwave absorbing materials.