Developing a scientific environmental management system is the institutional foundation to address transboundary environmental governance issues. Based on the perspective of cross-regional pollution control, this paper empirically analyzes the impact of the reform of the division and adjustment of environmental protection supervision powers between the central and local governments on cross-regional pollution control. The results show that both significantly reduce the air pollution emission level of the border prefecture-level cities, but the emission reduction efforts of the provincial border prefecture-level cities are lower than the overall average. From the perspective of the institutional reform of this study, in order to realize the compatibility of incentives for intergovernmental environmental governance at all levels, it is necessary to promote the reform of the environmental protection management system with the optimization of the division of intergovernmental environmental protection powers as the core, and improve the performance of cross-regional pollution control.