Port-hinterland transport is a freight transport mode that links ports and inland destinations and contributes to a large portion of the total CO₂ emissions from the entire port-related logistic chain. Infrastructure development is conducive to reducing transport emissions. However, decision making regarding the development of port-hinterland transport infrastructures is complicated because port throughputs for different types of cargo change with economic structural changes (ESCs) in the port’s hinterland. Therefore, this study develops a hybrid econometric and system dynamic model to explore the impact of ESCs in the hinterland on a port’s throughput and to formulate suitable infrastructure decisions to reduce CO₂ emissions from port-hinterland transport. The hybrid model is applied to the Qingdao port and its hinterland transport in Shandong Province, China. The results show that long-term CO₂ emissions from port-hinterland transport will increase significantly because Shandong’s ESCs will lead to a notable increase in the freight volume of containers, despite a concurrent decrease in the freight volume of iron ore. To reduce port-hinterland transport emissions under ESCs, facilitating railway transport for containers prioritizes over other options. The results also reveal that whether the ESCs are considered will lead to different infrastructure decisions, and whether life-cycle emissions of infrastructure are considered may lead to different priorities of infrastructure options. The findings indicate that holistic view and collaboration among government entities and transport-related stakeholders should be emphasized in the decision making of transport infrastructure development.