The article deals with the problem of using digital twins and digital threads in complex distributed cyber-physical systems with a high level of structural and functional dynamics. A three-level model of the life cycle of a complex cyber-physical system is proposed. At the upper level, the observed system is described in terms of a continuous architecture. At the middle level, the observed system is described in terms of an agile architecture. At the lower level, the observed system is described in terms of a multigraph, which allows describe both the observed system structure and behavior. In the case study the solution of the problem of monitoring the state of the subway infrastructure is considered. The proposed approach has shown its effectiveness and can be applied in other domains such as smart cities.