In recent years, scientists have found that some metal elements doped diamond-like carbon (Me-DLC) films can form a special self-organized layered nanostructure in the deposition process. This nanostructure can overcome the complexity and limitation of artificially controlled preparation for multilayer films, and endow the films more excellent performance. Here, the formation mechanism and influencing factors of the self-organized multilayer (SOM) structure in Me-DLC films were mainly illustrated. The effects of metal types, metal contents, deposition conditions (pulse frequency, substrate bias, flow ratio, deposition temperature and deposition time) and deposition methods on the formation of SOM structures and dimensions of metal-rich layer thickness, carbon-rich layer thickness, layer number, etc. were elaborated. Four types of the formation mechanisms for the SOM structure consisting of the ion rearrangement, the metal catalysis, the induction by strong ion irradiation and the target poisoning were emphatically introduced. Moreover, some deficiencies in the current research work were also discussed. For instance, the formation mechanism of the SOM structure was unclear yet. All of the four mechanisms mentioned above had limitations, and it was still a scientific difficulty to realize the internal control of the SOM structure by designing process parameters. On this basis, the further researches of the SOM structure in carbon-based films were also proposed.