As an important part of a modern economic system, a modern industrial system is the key to promoting high-quality economic development. China’s modern industrial system construction focuses on industrial restructuring. At present, in order to strengthen the support and leading role of transportation in the modern economic system, China is actively promoting the construction of a competitive transportation power. Therefore, it is necessary to study whether large-scale investment in transportation infrastructure can promote industrial structure transformation and upgrade. This paper takes China as the research background. Firstly, a RAM model was employed to evaluate the unified economic and environmental efficiency of transportation infrastructure that measures the level of transportation infrastructure investment. Secondly, a PVAR model was built to evaluate the dynamic effects of transportation infrastructure investment on industrial structure transformation and upgrade. Finally, from the perspective of rational flow and optimal allocation of resource factors, the paper points out that transportation infrastructure investment can indirectly promote industrial structure transformation and upgrade through three paths, namely expanding market demand, reducing resource misallocation and increasing technological innovation, and the first half of these paths are positively regulated by policies. Then, an empirical test was done with the moderated mediation model. Research findings suggest that: first, improvements in the unified economic and environmental efficiency of transportation infrastructure can only promote industrial structure supererogation in a short time, but have no significant effect on promoting industrial structure rationalization in the short or long term. Second, in actual situation, transportation infrastructure investment can promote industrial structure transformation and upgrade only by expanding market demand and technological innovation, but not by reducing resource misallocation. Third, the first half of these paths through which transportation infrastructure investment promotes industrial structure transformation and upgrade are positively regulated by policies. This paper provided some theoretical reference for promoting industrial structure transformation and upgrade by virtue of the sustainable development of transportation.