Abstract: At the current stage, it is still in the exploration period for the collaborative governance of pollution and carbon reduction to be incorporated into the ecological environment management system. Under the existing institutional framework, the management mechanism and technical methods are relatively lagging. The main challenges in the process of incorporating the collaborative governance of pollution and carbon reduction into the ecological environment management system were analyzed. By clarifying the responsible subjects, boundary scope and functional positioning, etc., of each institution, the collaborative governance framework for pollution and carbon reduction based on the ecological environment management system was analyzed. Applying the management and technical elements in the main institutional links of the existing ecological environment management system and aiming at the problems, some countermeasures and suggestions were put forward. In terms of source prevention and control, combined with the relevant pilots of collaborative governance of pollution and carbon reduction, the boundary scope, work content and management mechanism of carbon assessment in Three Lines One Permit (TLOP), planning EIA and project EIA should be improved; in terms of process control, the further construction of integrated management of pollutant emission permit data should be considered; in terms of law enforcement and supervision, the ways such as establishing a national carbon monitoring system should be explored to improve the enforcement effectiveness of law supervision, strengthen the mechanism of supervision and accountability, and promote the construction of a cooperative system for reducing pollution and carbon emission.