Abstract: The key for system of systems (SoS) operation is command and coordination under information-based con- dition. According to varied types and interactions of Agents in the operation systems, a super-network model of SoS operation, composing of triple networks of physics domain, information domain and cognitive domain, has been con- structed in this paper. Then we built command cycle model utilizing the operation-command-process characteristics of striding multi-domain and periodicity, and focused on the in°uence of the information exchange rhythm on e±ciency of the operation commanding based on the analysis of routines of information exchange. Furthermore, we modeled syn- chronization in SoS operation on the research of OODA operation loop in the application of Super network model and evaluated the capability of coordination by the order of synchronization of operation loops. Finally, experiment has been made to analysis the mechanism of command and coordination by utilizing the simulating data collected from the human-in-the-loop manoeuvre.