The study focuses on developing scientifically sound approaches to the strategic management of port infrastructure recovery and integration in the new regions of the Russian Federation into a unified national transport system. The methodology is based on a systemic analysis of organizational and economic mechanisms, resource provision, and adaptation of modern management models under geo-economic changes and sanctions pressure. The research identifies key systemic contradictions in coordinating the interests of the state and private investors, resource allocation, and the implementation of best practices. A conceptual model of integrated management is developed, including differentiated public-private partnership mechanisms, flexible strategic planning, and a multi-level performance evaluation system. The practical significance of the study lies in the formation of a set of recommendations for authorities and corporate structures aimed at ensuring the sustainable development of port complexes and strengthening the country's transit and logistics potential.