Inter-provincial administrative boundary areas are particularly vulnerable to ineffective regional pollution governance because they are simultaneously affected by transboundary pollution diffusion and administrative fragmentation. Existing governance practices, however, continue to rely heavily on territorially based regulation and administrative coordination, while the potential of cross-regional green-technology collaboration to address boundary pollution has received insufficient attention. Using panel data for Chinese prefecture-level cities from 2011 to 2023, this study systematically examines the impact of green innovation collaboration (GIC) on pollution control in areas along interprovincial administrative boundaries through two-way fixed-effects, instrumental-variable, Heckman two-step, and spatial Durbin models. The results show that, first, GIC significantly reduces pollution in these areas, and this finding remains robust across a range of robustness checks. GIC also generates significant spatial spillovers: while reducing local boundary pollution, it improves air quality in neighboring cities. Second, the heterogeneity analysis indicates that this effect is more pronounced in cities facing greater pollution-control pressure, lower fiscal pressure, and higher levels of openness. The regional results also reveal certain differences. Third, the mechanism analysis shows that cross-regional collaborative governance and industrial upgrading constitute two relatively independent parallel transmission pathways rather than a sequential chain, and their relative contributions vary with city conditions. These findings provide empirical evidence for improving interprovincial collaborative governance, facilitating the cross-regional diffusion of green technologies, and implementing differentiated environmental policies.