Novel peapod-like Co@carbon and Co(3)O(4)@carbon composite nanostructures have been successfully fabricated for the first time based on rational design and elaborate analyses. The nanostructures exhibit the unique feature of Co or Co(3)O(4) nanoparticles (20 nm) encapsulated inside and well-graphitized carbon layers coating outside. The peapod-like Co@carbon and Co(3)O(4)@carbon nanostructures exhibit intriguing morphologies, architectures, and chemical compositions. What is more important, the unique morphologies, architectures, and chemical compositions will lead to perfect performances in many applications. In this paper, a good example of Li-ion battery testing is given to demonstrate the superior stability and rate capability of the Co(3)O(4)@carbon. The peapod-like nanostructure of Co(3)O(4)@carbon demonstrates very high specific capacity (around 1000 mAh/g at the charge/discharge rate of 1C) and wonderful cyclability (at least 80% retention is available when cycled back from very high charge/discharge rate of 10C) during the galvanostatic cycling, indicating it as the promising candidate for Li-ion batteries' anodes. Additionally, the excellent electrochemical performance is significantly associated with the unique architecture in the samples, which verifies the feasibility of rational design of hierarchical materials for the actual applications. Meanwhile, the Co@carbon and Co(3)O(4)@carbon nanostructures demonstrate the regular and uniform distribution of magnetic nanoparticles in well-graphitized carbon fiber, which is a great achievement in the field of monodispersing and isolating magnetic nanoparticles. The prepared samples can also be potentially applied in other fields, such as gene delivery, catalysis, and magnetism.