The SO2 emission sources of the Chengdu-Chongqing economic zone were divided into 556 emissions units according to four different categories, which are city, industry, point sources, and area sources. The CALPUFF model was used to calculate the contribution of each unit, and consequently obtain an influence-transferring matrix. To ensure that the SO2 concentrations of 46 cities and counties in the Chengdu-Chongqing economic zone meet air quality standards, an emission optimization model was developed to calculate optimal emissions of each emission unit under different development scenarios. The result showed the optimal emissions of SO2 by different provinces and industries. To achieve the target of restricting and optimizing development, corresponding planning programs were developed for every district.