As a new type of environmental regulation implemented independently by local governments in recent years, the River Chief System (RCS) has become an important institutional innovation for the coordinated development of the economy and environment. However, most scholars only pay attention to the contribution of the river chief system in the field of water governance and ignore the changes made to regional carbon control. Based on panel data from 282 cities in China from 2007 to 2019, a time-varying DID was used to assess the policy impact of RCS on urban carbon emission efficiency. Our study found that: (1) The RCS has improved the efficiency of urban carbon emissions through industrial structure upgrading and green technology innovation. (2) Heterogeneity analysis shows that central cities and nonresource- oriented cities are more susceptible to the influence of the RCS and improve carbon emission efficiency. More than that, cities with appropriate environmental regulation intensity can better leverage the carbon governance effect of RCS. (3) The RCS has formed an unexpected policy effect of “beggar thy neighbor” in space, and its effect has a time lag.