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Containerization and its impact on structural shifts in maritime transport have attracted the attention of maritime researchers. However, few studies address the impact of China’s current economic reforms and industrial structure upgrades on China’s container ports. To fill this gap, this article delivers new insights on the geographical evolution of China’s ports in international container transport during the upgrade of industrial structure. This study finds that path dependence is evident in the container shipping structure, and major regional connections are still present between China and the maritime regions of East-Southeast Asia, Western Europe, and North America. During the study period, the spatial dynamics of the international linkages of China’s container ports exhibited a tendency to develop from an initial monocentric structure to an isolated double-center structure, and then a polycentric clustering structure. Dynamic panel analysis shows there is a long-term significant equilibrium relationship between industrial structure upgrading and port container transport trade. Proxy indices including the industrial structure advanced index, the industrial structure comprehensive index and the essential evolution of industrial structure have positive effects on the improvement of port container transport trade.