Collaborative control of atmospheric pollutants and greenhouse gas emissions is one of the important tasks during the 14th Five Year Plan period. Based on the Panel data of 278 prefecture-level city from 2006 to 2021, the regional synergistic emission reduction effect of the carbon emissions trading system is discussed by using multi period double difference.It is found that the carbon emissions trading system can not only significantly decrease regional carbon emissions, but also reduce the PM2.5, and furthermore realize the synergistic emission reduction effect of greenhouse gases and atmospheric pollutants. Mechanism analysis shows that this policy achieves regional emission reduction synergy through technological innovation, technological transformation, and improvement of energy consumption structure. At the same time, the level of marketization will also affect the emission reduction effect of the policy. Through heterogeneity analysis, it is found that the synergistic emission reduction effect of non resource-based cities is stronger than that of resource-based cities.