Carbon-encapsulated nickel nanoparticles were used as the representative magnetic carbon-encapsulated nanoparticles for chemical functionalization. After oxidation with the mixed acid of H2SO4/HNO3 under a moderate ultrasonic bath, carboxylic acid groups (-COOH) were effectively generated on the fullerene-like carbon shells, which in turn were utilized to covalently link octadecylamine through an amide reaction. The whole chemical process is well characterized by many methods such as Fourier transform infrared spectroscopy, X-ray photoelectron spectroscopy, thermogravimetry-differential scanning calorimetry, transmission electron microscopy, and so on, and the self-consistent experimental results were obtained. The results suggested that the magnetic nanoparticles could be well protected, while their magnetic properties could be utilized to guide the transfer of the grafted functional species on the particle surface. This provides many possibilities for potential applications in chemical and biochemical fields.