In order to clarify the influence of methane concentration and deposition time on self-organized nano-multilayers, three serial copper-carbon films have been prepared at various methane concentrations with different deposition times using a facile magnetron sputtering deposition system. The ratios of methane concentration (CH4/Ar+CH4) used in the experiments are 20%, 40%, and 60%, and the deposition times are 5 minutes, 20 minutes, and 40 minutes, respectively. Despite the difference in the growth conditions, self-organizing multilayered copper-carbon films are prepared at different deposition times by changing methane concentration. The film composition and microstructure are investigated by x-ray photoelectron spectroscopy (XPS), x-ray diffraction (XRD), field emission scanning electron microscopy (FESEM), and high-resolution transmission electron microscopy (HRTEM). By comparing the composition and microstructure of three serial films, the optimal growth conditions and compositions for self-organizing nano-multilayers in copper-carbon film are acquired. The results demonstrate that the self-organized nano-multilayered structure prefers to form in two conditions during the deposition process. One is that the methane should be curbed at low concentration for long deposition time, and the other condition is that the methane should be controlled at high concentration for short deposition time. In particular, nano-multilayered structure is self-organized in the copper-carbon film with copper concentration of 10-25 at.%. Furthermore, an interesting microstructure transition phenomenon is observed in copper-carbon films, that is, the nano-multilayered structure is gradually replaced by a nano-composite structure with deposition time and finally covered by amorphous carbon.