Environmental regulation is an important way to address the negative externalities of environmental governance and to advance regional green innovation efficiency. This paper takes the panel data of 30 provinces and municipalities from 2011 to 2021 as the research object, adopts Super-SBM to measure the regional cross-border e-commerce green innovation efficiency (EGIE) in each region, utilizes the system GMM method to test the impact effect of environmental regulation on EGIE and the mechanism of its action, and carves out the dynamic evolution and spatial differentiation in terms of the time series of the spatial and temporal evolution of EGIE. The results show that environmental regulation significantly promotes the enhancement of EGIE at the 1% level (β = 0.105). In terms of the impact mechanism, environmental regulations increase EGIE by improving the level of industrial structure upgrading, and intellectual property protection negatively regulates the relationship between environmental regulations and EGIE (β=-0.270). Threshold analysis finds that there is a significant double threshold effect of industrial agglomeration on environmental regulations to promote EGIE growth. When the industrial agglomeration value (AGG≤0.0072) is active, it will promote the green innovation efficiency of cross-border e-commerce, but exceeding the threshold value of industrial agglomeration (AGG=0.0202) will weaken the promotion effect of environmental regulation on EGIE. The purpose of this paper is to study the impact effect of environmental regulation in addressing the relationship between environmental pollution control and promoting EGIE, with a view to providing a decision-making basis for the coordinated development of regional cross-border e-commerce and the environment.