Abstract: The mutual feedback relationship between the optimization of regional industrial structure and the enhancement of total factor productivity is crucial for improving resource allocation efficiency, promoting rural revitalization, and facilitating regional high-quality development. Special types of regions are key areas for advancing rural revitalization and high-quality development. This study selects three regions as samples and employs the Panel Vector Autoregressive Model (PVAR) to explore the evolutionary relationship between the optimization of regional industrial structure and the improvement of total factor productivity. The results indicate that: 1) Both the regional industrial structure and total factor productivity are trending positively. 2) The optimization of regional industrial structure and the enhancement of total factor productivity mutually reinforce each other, with the effect of industrial structure rationalization on total factor productivity being greater than that of industrial structure upgrading. The long-term mechanism indicates that after total factor productivity is positively impacted by the rationalization of industrial structure, it continuously supports industrial structure upgrading, which in turn promotes the enhancement of regional total factor productivity. 3) In the future, the improvement of regional total factor productivity and the optimization of industrial structure will primarily depend on their own developmental paths, with industrial structure upgrading contributing more to the enhancement of total factor productivity than rationalization. Based on this, recommendations are made regarding the development of diversified industries, the promotion of industrial structure transformation and upgrading, and the coordination and overall planning of spatial production, aiming to provide decision-making references for achieving regional high-quality development.