The integrated energy system in multi-station integration is an important means for power grid enterprises to reduce carbon emissions. Taking full account of economic constraints, operation characteristics constraints and security constraints, aiming at the lowest global carbon emission rate, and according to the characteristics of power grid enterprises, this paper defines the global low-carbon operation mode of integrated energy system in multi-station integration, and constructs a low-carbon strategy model based on robust model. The empirical mode decomposition method is used to mine the multi-dimensional historical data, generate the finite randomness scene, and carry out the deterministic optimization of the model. The particle swarm optimization algorithm is used to obtain the optimal solution of the global low-carbon strategy, that is, the daily low-carbon operation strategy. Finally, the example analysis proves that the method proposed in this paper can provide a scientific and feasible low-carbon operation strategy for the integrated energy system in the multi-station integration.