Owing to the large surface energy and easy agglomeration, ferroferric oxide (Fe₃O₄) nanoparticle usually is difficult to be widely application in microwave absorbing coatings. In this paper, a new synthesis process was used to prepare solvent-free fluid Fe₃O₄ (S-Fe₃O₄) by surface modification of solid Fe₃O₄ with a long chain of organic bimolecular layer, which showed excellent dispersion in resin materials. Moreover, S-Fe₃O₄ was compounded with CNT@Fe₃O₄ to prepare S-Fe₃O₄/CNT@Fe₃O₄/EP composites, which realized the multiple loss mechanism of electromagnetic wave (EMW) absorption. The results showed that the minimum reflection loss of composite was −52.57 dB with a matching thickness of 3.3 mm; the maximum effective absorption bandwidth at 1.4 mm thickness was 5.2 GHz (12.08–17.28 GHz). This surface molecular engineering composite based on inorganic particles enhanced the attenuation ability of EMW by improving the dispersion of inorganic particles and providing multiple loss mechanisms, which was a novel medium regulation strategy to provide a new insight for nanoparticles in the field of EMW absorbing coatings.