From a global perspective, carbon emissions are a global problem that needs to be solved urgently. At present, 61% of countries have committed to achieving net zero emissions. Compared with industry and construction, the transportation sector has become the focus and challenge for countries to achieve carbon neutrality due to the characteristics of strong mobility, scattered emission sources, and complex social behaviors. Therefore, the issue of carbon emissions in the transportation industry has become the focus of academic attention. This paper first calculates the carbon emission efficiency (CEE) of the regional transportation industry through the super-efficiency SBM model and then evaluates its regional differentiation characteristics through the Theil index, which has important practical significance for reducing regional carbon emissions. The results show that the national transportation CEE average value is 0.612, a relatively low level. The spatial distribution of China’s transportation CEE shows an obvious characteristic of “east highest and west lowest”. The regional differences in the transportation industry CEE are larger than those between regions. The differences in the transportation industry CEE among the eastern, central, and western regions are on the downward trend as a whole, and intra-regional differences are greater than inter-regional. The intra-regional differences cause the overall differences in transportation industry CEE; the eastern region contributed the most to the Theil index, while the central contributed the least. The biggest factor affecting the transportation industry CEE is the regional energy structure, and the smallest factor is the per capita GDP. This research has important reference significance on the target of carbon neutrality.