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Byline: Dmitry Ivanov In the framework of Supply Chain (re)-Design (SCD), different structures (functional, organisational, 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. For the conceptual and mathematical models, we propose to apply 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 inter-disciplinary treatment allows comprehensive and realistic SCD problem formulation and solution. We emphasize the flexibility of the proposed approach and optimisation-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.