As carbon emission continue to rise and climate issues grow increasingly severe, countries worldwide have taken measures to reduce carbon emission. However, carbon dioxide is continuously flowing in the atmosphere and is easily influenced by neighboring cities' policies. Therefore, how to solve the problem of carbon emission spillover effect has become the key to improve policy efficiency. Cross-regional carbon governance provides a perspective on solving the carbon emission problem by regulating and guiding the cooperative behavior of cross-regional governance actors. Taking Chengdu-Chongqing area as an example, this study used the SDM to analyze the influencing factors and spatial spillover effects of emission. Then we used the system dynamics method to construct a dual-core carbon emission system, and simulated the spillover effect and emission reduction potential of Chengdu and Chongqing emission reduction policies under different policy schemes. The results reveal that the mobility of population and enterprises have a significant impact on carbon emission prediction. Carbon reduction policies exhibit the phenomena of "carbon transfer" and "free-riding." When Chengdu lowers its economic growth rate, it leads to the transfer of high energy-consuming enterprises to Chongqing, increasing carbon emission in Chongqing. The implementation of comprehensive carbon reduction policies in Chongqing has a positive effect on Chengdu. Emission reduction policies exhibit issues related to their temporal efficacy, as the effects of industrial structural policies in Chengdu yield opposite outcomes in the short and long term. Each city's unique circumstances necessitate tailored carbon reduction policies. In order to reduce carbon emissions, Chengdu and Chongqing require opposite population policies.