Abstract Body-centered cubic (bcc) phase iron nanocrystals with granular, rod-like and flaky shapes were prepared through a simple surfactant-controlled chemical reduction route. In view of extra stability and enhanced manipulative ability, thus-prepared iron nanoparticles were morphology-retained modified with a thin silica shell through a Stober process. A serial of techniques such as X-ray diffraction (XRD), field emission scanning electron microscopy (FESEM), transmission electron microscopy (TEM), Fourier transform infrared spectrometer (FTIR), X-ray photoelectron spectrometer (XPS), thermogravimetry (TG), vibrating sample magnetometer (VSM) and scalar network analyzer (SNA) were used to characterize the iron particles before and after silica coating. Results showed that the surface silica coating could effectively improve the oxidation resistance and microwave absorption performance of iron particles, while slightly influenced their magnetic properties. Furthermore, the flaky Fe@SiO2 nanocapsules particles exhibited better microwave absorption performance than that of the granular and rod-like counterparts, which could be ascribed to the shape effect.