As the main form of digital trade, cross-border e-commerce has become an important factor influencing China’s green and low-carbon transition. This article used the multi-period Difference-in- Differences (DID) method to comprehensively examine the effect of cross-border e-commerce on urban carbon emissions based on data from 283 cities in China from 2009 to 2019. The results showed that cross-border e-commerce can significantly reduce urban carbon emissions. However, there is significant heterogeneity in the effect of cross-border e-commerce on urban carbon emissions due to differences in digital infrastructure, environmental regulatory intensity, geographic location, and city level. Further mechanism testing found that cross-border e-commerce primarily reduces carbon emissions through green technological innovation and industrial structural upgrading. This article provides directional insights for the future development of cross-border e-commerce comprehensive pilot zones and offers empirical evidence for China to promote the coordinated development of environmental protection and trade.