Abstract: Aiming at the low-carbon economic dispatch of the integrated energy system, this paper constructs a low-carbon economic operation framework of the comprehensive energy system with multiple micro integrated energy systems, and a two-level optimal dispatch strategy of the integrated energy system considering the green certificates-carbon trading mechanism is proposed. Firstly, the carbon emission intensity and carbon emissions of each node in the energy network is calculated, which utilize the carbon emission flow model. Secondly, by analyzing the operation mechanisms of carbon trading and green certificate trading markets, the carbon trading, green certificate trading model of the micro integrated energy system are established, and green certificate-carbon trading linkage mechanism is designed to reduce the carbon trading fulfillment costs of micro integrated energy system. Then, a two-layer optimal dispatch model of integrated energy system under green certificate-carbon trading mechanism is established. The upper layer is the economic dispatch model of power grid and gas network. The lower layer is the low-carbon economic dispatch model of multi micro integrated energy systems considering the demand response with the goal of minimizing the operating cost. Finally, the calculation example shows that the proposed model can effectively reduce carbon emissions, decrease renewable energy waste, and achieve lowcarbon economic operation of the integrated energy system.