Under the guidance of resource conservation and ecological environmental protection strategies, in order to improve transportation efficiency, optimize transportation structure, and achieve environmental friendly and sustainable developments of transportation industry, the factors affecting the transportation structure efficiency are analyzed from the two aspects of traffic input and system output. By introducing the super-SBM (slack based measure) undesirable model, which considers the environmental benefits of the transportation structure system, the transportation structure efficiency of 30 provinces in China is systematically analyzed. Then, the Tobit regression and geographically weighted regression method are used to analyze the causes of transportation structure efficiency differences, the spatial differentiation of factors, and accordingly propose the adjustment strategies for the transportation structure. The results show that the comprehensive efficiency of transportation has obvious regional differences. The top five provinces are Shanghai (1.567), Guangdong (1.366), Yunnan (1.292), Jiangxi (1.181) and Anhui (1.160). The regression coefficients in terms of the proportion of secondary industry output in GDP, population density, and regional per capita GDP are 0.9513, 0.7659 and 0.5691 respectively, which have the most significant impact on the transportation structure efficiency. The spatial distribution of sub-variable coefficients shows that there is spatial heterogeneity for different regions in the influence level of socioeconomic factors on the transportation structure efficiency. To improve the overall transportation efficiency in China, it is necessary to transform the large-scale and rough development of transportation infrastructure into the refined design and planning of transportation layout, optimize resource allocation, and promote the development of public transportation. Copyright ©2021 JOURNAL OF SOUTHWEST JIAOTONG UNIVERSITY. All rights reserved.