Aiming at the problems of environmental pollution and the conflict of interests of multiple energy suppliers in the integrated energy system, an economic analysis model of the integrated energy system based on cooperative game under the carbon trading mechanism is proposed. Firstly, in order to control CO₂ emissions, a cooperative game model with three energy supplying entities, including renewable energy power plant, carbon capture power plant and gas-fired thermal power plant, is established by introducing the carbon trading mechanism, and the optimization objective of the model is to minimize the sum of operation and maintenance cost, penalty cost, carbon related cost and environmental cost. In order to rationally allocate the cooperative costs of multiple energy supply subjects, the Shapley value method is firstly used for the initial allocation. Then, a correction factor that integrates the cost contribution coefficient and environmental contribution coefficient is introduced to further optimize the initial allocation results, and an improved Shapley value method apportionment mechanism is proposed. The simulation results show that the cooperative operation of the energy entities can effectively enhance the new energy consumption capacity, promote the complementary utilization of multiple energy sources, and significantly improve the system economy and reduce carbon emissions, and the improved Shapley value method can make the cost sharing among the energy entities more fair and reasonable.