The Internet of Things connects many articles such as equipments and facilities of various industries. There are many problems about how to manage these nodes effectively and to ensure high clock synchronization precision. The clock synchronization architecture of Internet of Things is the key technology to resolve these problems. In this paper, a new clock synchronization architecture of network for Internet of Things is suggested. In this new clock synchronization architecture, it includes three levels: adaptation level, organization level and region level. The adaptation level architecture is to resolve the problem about the adaptability of Internet of Things; The organization level architecture is to organize and manage of the clock synchronization system; The region level architecture is to ensure clock synchronization accuracy and security. At last the relationship of there level architectures is descript based on graph theory, an experimental system is suggested.