To promote the construction of a new energy system and facilitate the realization of the "dual carbon" goal, a rational and optimal allocation of energy system is essential. This paper introduces an optimal configuration method of integrated energy station considering low-carbon operation. Firstly, the factors influencing the location of the energy station are analyzed, the Voronoi diagram and the hollow circle strategy are used to determine the candidate location set of integrated energy stations, and the final installation location is determined according to the minimum integrated load moment. Then, a multi-objective optimal allocation model with the least total annual cost and carbon emissions in terms of both environmental and economic benefits is developed with the type and capacity of the equipment allocated to the integrated energy station as the decision variables, and an improved fast non-dominated ranking genetic algorithm with elite strategy (NSGA II) is proposed to solve the model. Finally, for the diversity of Pareto solution sets, the fuzzy subordination method is used for decision making. The simulation results of the algorithm prove that the proposed candidate locations can reduce the search space of the optimal solution, and the established optimal configuration model is feasible and effective, which can reflect the economy and carbon reduction effect of the integrated energy station.