As world resources and environmental constraints have increased, environmental cost has become a concern that affects the sustainable development of the logistics industry in various countries. Carbon emissions are an important part of any environmental cost assessment. How to scientifically and rationally evaluate the green GDP impact and regional efficiency in the logistics industry, especially when under carbon emission constraints, is of great significance to the realization of green and sustainable development. This study evaluated the logistics efficiency of 30 provinces in China from 2003 to 2016 by constructing a super SBM (Slack Based Model) model with undesirable output to explore provincial efficiency and its regional differences. The input–output ratio of the regional logistics industry was optimized through the calculation of the frontier slack variables. The research results showed that, first, it was more reasonable to adjust efficiency under carbon constraints, and it was consistent with the actual performance of the logistics industry. Second, technological progress and deeper capital investments promoted the development of the logistics industry, but technological barriers and low-scale efficiency between regions often limited technological efficiency. Therefore, decision-makers in the logistics industry should reconsider the challenges presented in each reason, encourage industrial technological innovation between regions, and especially promote energy-saving and emission-reduction technologies, so as to maintain the sustainable growth of the logistics industry.