This paper focuses on the spatial structure convergence of China's transportation system from 1978 to 2016 using the sequential panel selection method (SPSM). The contribution of this research is that the convergence order and the factors affecting the difference in convergence rates are analysed using improved econometric methods. Our robust conclusions show the convergence of China's transportation structure within different provinces, except for Hubei province. In terms of the different regions, the eastern and western regions have local convergence characteristics, while the central region presents non-convergence characteristics, especially in Henan, Hei Longjiang, Jilin, Anhui, and Hubei provinces. The spatial spillover characteristics of transportation structure convergence are most obvious in northwest China. We also examine the main factors that influence the rate of convergence and find that urbanization promotes the convergence of the transportation structure, while local protectionism hinders the spatial convergence of the transportation structure. Additionally, China's transportation infrastructure is more policy-driven than economics-driven. This study provides a reference study for analysing the regional development balance of China's transportation structure and regional differences.