Abstract: With the continuous promotion of carbon peaking and carbon neutrality goals in China, to promote the consumption of renewable energy and reduce the carbon emission of the system, this paper proposes a green certificate-carbon emissions trading interaction model based on cooperative game theory for an integrated energy system from the perspective of joint efforts of power generation, carbon sequestration, and the market mechanism. The simulation is carried out in an integrated energy system in eastern Inner Mongolia. In this model, the generation side realizes the flexible interaction between the carbon capture power plant and the renewable energy generation entity with the advantage of centralized dispatching of the integrated energy system（IES）; the carbon sequestration side realizes the low carbon economic operation of IES through carbon capture equipment and power-to-gas equipment（P2G）; the market side improves the integral economy of IES through the establishment of the green certificate-carbon emissions trading interaction mechanism, and based on the Shapley value to reasonably allocate the cooperation surplus. The results show that the proposed method can significantly reduce the system power curtailment, make full use of deep peak-regulation of thermal power units, realize the low-carbon economic operation of IES, and provide a theoretical reference for exploring the feasibility of cooperation between the existing thermal power and renewable energy projects, and exploring a new way of coal-fired power plant flexibility transformation.