Adjusting transportation structure to reduce the intensity of greenhouse gas emissions is an effective way to address climate change issues. This paper selects six transport sectors and constructs a hybrid input-output model to study the impact of transportation restructuring on the intensity of CO₂ and non-CO₂ greenhouse gas emissions in each sector during different periods. The results show that the effect of transportation restructuring on greenhouse gas emissions is manifested differently in different time periods. After 2008, transportation restructuring had a significant effect on reducing the intensity of greenhouse gas emissions in all sectors. However, the impact of transportation restructuring on the intensity of non-CO₂ greenhouse gas emissions is limited. It is also found that the railway transport sector has been a low-impact transport sector in terms of greenhouse gas emissions since 2004, which provides insights for the optimization of China’s transportation structure.