In the framework of supply chain (re)- design (SCD), different structures (functional, organizational, informational, etc.) are (re)- formed. These structures are interrelated and change in their dynamics. How is it possible to avoid structural incoherency and consistency and to achieve comprehensiveness by (re)- designing supply chains? This paper introduces a new approach to simultaneous multi-structural SCD with structure dynamics considerations. We elaborate a new conceptual model and propose new tools for multi-structural SCD – multi-structural macro-states and dynamical alternative multi-graphs. The research approach is theoretically based on the combined application of operations research, agent-based modelling, and control theory. The results show the multi-structural and interdisciplinary treatment allows comprehensive and realistic SCD problem formulation and solution. We emphasize the flexibility of the proposed approach and optimization-supported simulation. The proposed methodology enhances managerial insight into supply chains at the strategic and tactical levels and serves to assist decision-makers in SCD.