Global climate change has prompted research on carbon emissions (CEs), with the freight transportation sector in China exhibiting a significant increase in CEs. This study aimed to optimize the freight structure in China and to develop a low-carbon freight transportation system. As one of the main factors influencing freight CEs, research on the freight structure is helpful for understanding the comparative advantages and potential environmental impacts of various freight transportation modes. The freight structure was characterized by calculating the proportion of the freight turnover of four transportation modes, and the mechanism of the influence of the freight structure on freight CEs was examined by combining the Stochastic Impacts by Regression on Population, Affluence and Technology model and geographically and temporally weighted regression model. It is worth noting that from 2005 to 2023, the transport carbon intensity (CEI) has decreased significantly in some provinces, such as Beijing and Tianjin Province, by 22.94% and 75.49%, respectively. But freight costs in both Hebei and Gansu have risen by more than 65%. Nevertheless, the overall freight CEI in China has decreased by approximately 25.69% over the past 15 years due to freight transportation mode and technology advancements. The findings provide valuable insights for establishing government transport policies to reduce freight CEs and promote sustainable transport systems. Emphasizing the importance of restructuring freight transport, this study offers a methodological framework for future research, and strategies are proposed to reduce CEs from the perspectives of institutional adjustment, potential direction exploration, and policy incentives.