As a key export-oriented economy, China faces significant challenges to its green economic development due to industrial pollution. While digital trade is crucial for sustainable development, its impact on industrial pollution has not been studied. This paper addresses this gap by adopting prefecture-level data from 2005 to 2021 and using a staggered difference-in-differences model to assess the impact of comprehensive pilot zones policy of cross-border e-commerce (CBEC) on industrial sulfur dioxide pollution. The findings indicate that CBEC significantly reduces industrial sulfur dioxide emission intensity, with the effect growing stronger over time. The effect is particularly notable in eastern and western regions, large cities, cities with underdeveloped digital infrastructure, and cities with lower pollution. Mechanism analysis reveals that CBEC lowers industrial emission intensity by driving structure upgrading, fostering green innovation, and advancing digital transformation. This paper emphasizes that the government can expedite the green transformation of the economy by integrating digital trade with industry.