Fabrication of Nano-multilayered structure film is often complex owing to its fabricated process which needs to regulate a certain deposition parameter periodically. Here, we demonstrated a self-organized nano-multilayered structure in carbon-copper thin films only using one single sputtering target of copper in a conventional DC reactive sputtering deposition process. The influence of methane concentration on the microstructure, especially on the self-organized nano-multilayer, of the films were investigated by X-ray photoelectron spectroscopy (XPS), Raman spectroscopy, field emission scanning electron microscopy (FESEM) and high-resolution transmission electron microscopy (HRTEM). The results showed that the film deposited at low methane concentration was consisted of disorder copper grains with higher copper content. With increasing methane concentration, the copper content in the films decreased and the film structure was gradually transformed to a self-organized nano-multilayered structure consisting of alternating carbon and copper nanolayers. Based on (a) the effect of carbon adsorbed on the copper target leading to target poisoning, (b) the influence of copper grain size and crystallinity orientations on surface roughness of interface between carbon-rich and copper-rich layer and (c) the low energy ion bombardment enhanced inter diffusion, the mechanism of self-organized formation of nano-multilayer in the carbon-copper thin films was proposed.