Fe3O4@SiO2 composites with different morphologies (hollow nanorods, porous nanorods, and flower-like nanoparticles) were constructed using different preparation methods. Considerably enhancement of resonance frequency and permeability beyond Snoek’s limitation were observed in the Fe3O4@SiO2 composites with shape anisotropy and porous core-shell nanostructure. The resonance frequency of porous Fe3O4@SiO2 nanorods enhanced to 4.21 GHz, which is much higher than the natural resonance frequency of 1.2 GHz for Fe3O4 bulk. The minimum reflection loss (RLmin) of Fe3O4@SiO2 porous nanorods reached -59.49 dB at 8.89 GHz, and its effective bandwidth (RL < -10 dB) covered 4.52 GHz at a thickness of 3.18 mm. In addition, the radar scattering cross section (RCS) reduction value reached more than 48 dBm2 after removing the background. Our study provides insight into the relationship between anisotropy, core-shell structure, morphology of nanoparticles and corresponding microwave performance, and provides a reference scheme for the fabrication of high-performance lightweight microwave absorbing materials.