Based on the perspective of total factor productivity and the unexpected output of carbon emissions, this paper measures transportation total factor carbon emissions efficiency during 2003-2015 by applying DEA Super-SBM. And the internal driving and external shock effect of industry carbon emissions is investigated to explore the influence factors and dynamic conduction mechanism of transport carbon emissions efficiency by IGVAR. Empirical conclusions show that emissions efficiency of transportation industry is higher than that of mining, manufacturing and electric power, heat, gas and water production and supply industry, but significantly lower than that of agriculture and construction. With regard to internal driving factors in transportation, economy size and technological progress have significant effects on carbon emissions efficiency, and energy structure is not significant. From the perspective of effects between industries, economy size, energy structure, technical progress is obvious in manufacturing and construction, but very faint in other industries. The effect of industries technology progress is positive, and the effect of economy size and energy structure of construction are positive, and the effect of manufacturing is negative. In order to promote carbon emissions efficiency, a mechanism of division of responsibility among different industries should be established, with the policy of energy-saving and emission-reduction in transportation industry.