With the advancement of wireless technology, there is a significant need for magnetic/carbon nanocomposites capable of absorbing electromagnetic waves across a wide frequency spectrum. However, designing these absorbers with uniformly distributed magnetic nanoparticles without agglomeration, to obtain optimal magnetic loss performance remains a significant challenge. In this work, FeCoNiCuMn alloy nanoparticles encapsulated in a graphitic C-shell have been successfully synthesized using metal-organic chemical vapor deposition. The incorporation of magnetic nanoparticles boosts magnetic loss, complementing dielectric loss to optimize electromagnetic waves attenuation, while the core/shell architecture further improves impedance matching. Moreover, adjusting the Mn contents enables the regulation of absorption performance in terms of thickness and working frequency. Thanks to their optimized impedance matching and multiple loss mechanisms, the FeCoNiCuMn0.5/C nanoparticles showcased outstanding attenuation capabilities. This included achieving a reflection loss of −52.30 dB at a thickness of 2.35 mm and an effective absorbing bandwidth covers 5.52 GHz at 2.0 mm. Moreover, the coatings containing FeCoNiCuMn0.5/C nanoparticles contributed to notable reductions in radar cross-section values, with the most significant reduction reaching up to 26.04 dBm2. This study highlights the potential practical application of FeCoNiCuMn nanoparticles encapsulated within a graphitic C-shell as highly efficient electromagnetic wave absorbing materials.