Extensive research has been carried out on the “Belt and Road” initiative, most of it focusing on geographical economy and international trade. However, there is a lack of research on the carbon emissions efficiency of the countries along the “Belt and Road,” especially regarding the impact of freight trade. To address this research gap, this paper first employs a metafrontier nonradial directional distance function to measure the carbon emission efficiency of 32 countries along the “Belt and Road” from 1990 to 2014. It then examines the role of freight trade. Our main research findings are as follows. Firstly, the carbon emission efficiency of the countries along the “Belt and Road” is generally low. Among them, Russia and Central Asia are mainly due to the large between-group gap in carbon emission efficiency, while Southeast Asia, Western Asia and North Africa, East Asia, South Asia, and Central and Eastern Europe are mainly due to the large within-group gap. Secondly, freight trade promotes carbon emission efficiency, but it will aggravate the gap between the contemporaneous technology and the group technology. Freight trade mainly promotes the contemporaneous carbon emission efficiency (CTCEI) and group-frontier carbon emission efficiency (ITCEI) of low fossil energy dependent countries, and the metafrontier carbon emission efficiency (GTCEI) of high fossil energy dependent countries. Thirdly, foreign direct investment (FDI) has a significant negative effect on a host country’s ITCEI and GTCEI, and it will decrease the gap between the group technology and the metafrontier technology. However, freight trade can effectively prevent the entry of FDI, thereby indirectly improving carbon emission efficiency and reducing carbon emission gap.