Responding to the critical need for stable microwave absorption (MA) devices in complex and extreme environments, dual-function electromagnetic wave absorbers have garnered significant attention. Addressing this, we developed a novel FeNi-based composite encapsulated within superhydrophobic SiO2@Perfluorooctyltriethoxysilane (F13)/Methyltrimethoxysilane (MTMS) hybrid capsules, approximately 28-nm-thick, utilizing a straightforward one-pot strategy. This innovative FeNi@SiO2@F13/MTMS composite surpassed pure FeNi, exhibiting an effective MA bandwidth of 8.16 GHz and a minimal reflection loss value of −24.03 dB at 2.00 mm. It also boasted the largest radar scattering cross-section reduction value recorded at 21.09 dB m2. The enhanced MA properties were primarily attributed to the SiO2@F13/MTMS, which significantly improved the substrate's impedance matching. In addition to facilitating multiple scattering and reflection, it also triggered dipole and interfacial polarization. Moreover, the SiO2@F13/MTMS layer was instrumental in reducing the corrosion current density of FeNi from 3.512 mA cm2 to 5.59 nA cm2, thereby demonstrating exceptional corrosion resistance. This remarkable improvement was largely due to the surface hydrophobicity and the barrier effect provided by the hybrid capsules. Our exploration into corrosion-resistant and efficient MA materials provides valuable insights for the rational design of bifunctional components tailored for specific applications.