This paper deals with the problem of System-of-Systems (SoS) modeling whose structure change due to thedynamics of its constituent systems as they are developed in different operating modes. Designed by usingmulti-model approach, each operating mode represents a process functioning of its system, depending on theresources to activate and requirements to enforce. Studied as a Discrete-Event System (DES), we propose ahierarchical framework for designing suitable switching control for dynamic SoS using the High Level PetriNets (HLPN). Following a bottom up approach, we model each component first in a separate sheet and thenthe operating modes. Next, systems are designed by integrating a switching mechanism to commit to differentoperating modes when switching events occur. Finally, a mechanism for managing systems dependenciesinside the SoS is proposed. Algorithms are provided to generate the different layers of HLPN permitting easyimplementation of our framework and a flexible manufacturing SoS is used to illustrate our approach.