Understanding the roles and regional differences associated with cleaner production (CP) and end-of-pipe treatment (ET) can provide valuable information for the reduction of pollutant emissions. Considering the differences of these impact pathways, this paper proposes a two-stage decomposition method for investigating the contributions of CP and ET to the reduction of pollutant emissions. This two-stage method enhances the accuracy and obtainable detail of the decomposition results. Then, empirical research was conducted by decomposing the changes of China's industrial sulfur dioxide (SO2) emissions during 2005–2015. At the national level, CP and ET both decreased Chinese SO2 emissions, and CP has become the dominant approach for SO2 emission reduction in 2010–2015. Moreover, coal pollution intensity and treatment strength are key factors that need to be improved in CP and ET, respectively. At the provincial level, CP exerts a stronger impact on SO2 emission differences among different regions, while ET exerts less impact on SO2 emission differences among different regions. Based on the decomposition results, this paper presents targeted policy implications..