Based on the energy consumption data of the logistics industry in 30 provinces and cities in China, this paper uses the carbon emission accounting method of IPCC to estimate the total carbon emissions of the logistics industry in China from 2010 to 2019, and introduces the carbon emission Theil index. The Logarithmic Mean Divisia Index (LMDI) model is used to measure the regional differences in carbon emissions of China’s logistics industry and decompose the influencing factors. The research results show that the total carbon emissions of China’s logistics industry have increased significantly, and the total carbon emissions and growth rates of the eastern region are significantly higher than those of the central and western regions. On the whole, the inter-provincial differences in carbon emissions of China’s logistics industry have not changed substantially and have shown a downward trend. Intra-regional differences are the main reason for the overall difference in carbon emissions in China’s logistics industry, and inter-regional differences have little impact on the overall difference. Among the three major regions, the eastern region has the largest inter-provincial carbon emissions difference, followed closely by the central region, with the western region having the smallest difference. Furthermore, the difference in carbon emissions between the eastern, central, and western regions is expanding, the results of the LMDI model show that the economic development effect is the most important positive effect of the logistics industry’s carbon emissions in terms of the national average. The population scale effect is second, and the energy intensity effect is the main negative effect, followed by the energy structure effect. In terms of regional differences, the energy intensity effect is the most obvious in the eastern region, and the population scale effect has a relatively greater impact on the western region. The effect of economic development on the eastern and western regions is higher than in the central region.