o improve the environmental and economic benefits of an integrated energy system, promote the consumption of renewable energy and stabilize system fluctuation, this paper proposes an optimal scheduling model of an integrated energy system considering waste incineration flue gas treatment and power-to-methanol conversion. First, in the waste incineration power plant, the desulfurization, denitrification, carbon capture and flue gas storage devices together constitute a flue gas treatment system to reduce environmental pollution and realize the decoupling of waste incineration power generation and flue gas treatment. Secondly, a coordinated operational framework of a flue gas treatment system-electric-to-methanol-methanol fuel cell is constructed. The CO2 obtained by carbon capture is used as the raw material of electricity-to-methanol, and the generated methanol can directly obtain the commodity income, and the power supply stability of the system can be maintained through the methanol fuel cell. Finally, a reward-penalty differential ladder carbon trading mechanism is proposed to constrain the carbon emissions of the system, and an optimal scheduling model with the goal of minimizing the net cost of system operation is established. The results show that the model has the effect of “peak load shifting” and can effectively promote the green and economic operation of the system.