Recently IMO and IALA have developed the strategy of e-Navigation and the concepts of VTM to enhance the safety, efficiency and security of vessel traffic and protection of the marine environment. And current technical and functional trends require vessel traffic management systems to be improved so as to control vessel traffic not only in waters of harbour area, but also within EEZ waters. Under the consideration of these circumstances, a three-layered vessel traffic management system was proposed in this paper. The proposed system consists of three sub-systems, called Local VTS, Regional VTS and National VTS, and those sub-systems are designed respectively to be suitable for managing vessel traffic within their own jurisdiction waters.