Recently, for electromagnetic wave (EMW) absorption materials, a considerable literature has testified the significant role of structures, composition, morphologies and interface in the enhancement of absorbing properties. However, far too little attention has been paid to the intensive research of surface morphology of Fe3O4 particles. The objective of this paper is to research the influence of Fe3O4 morphology on absorbing performance of Fe3O4/Multiwalled Carbon Nanotubes (MWCNTs) hybrids. The morphology of Fe3O4 particles was adjusted by the templating agent content of NH4HCO3 and NH4Ac in hydrothermal process. Of importance, we proposed to quantify the difference of Fe3O4 morphology by surface roughness. The surface roughness of three Fe3O4 particles are characterized by atomic force microscopes (AFM), which were 13.1 nm, 21.3 nm and 32.4 nm, respectively. The three absorbing hybrids were prepared via blending Fe3O4 particles with MWCNTs, and the minimum reflection loss (RLmin) of the three hybrids were −24.89 dB, −30.88 dB and −41.00 dB, respectively. The results indicated that the Fe3O4 with larger surface roughness tends to exhibit better EMW absorbing performance. It can be inferred that the greater roughness of Fe3O4 particles is an important factor to enhance EMW absorbing properties of Fe3O4/MWCNTs hybrids.