An energy efficiency evaluation method of exergy efficiency of integrated energy system considering primary energy permeability is proposed in this paper. Firstly, based on the input of the integrated energy system data set, an exergy efficiency evaluation model about energy efficiency is established, including the input exergy value model on the energy supply side and the output exergy value model on the energy consumption side. Among them, the input exergy value of external power grid purchase is determined on the basis of the permeability of primary energy, and the output exergy value model of the energy consumption side is considered in the output exergy value of cold, heat, electricity and natural gas load. Then, according to the ratio of the total exergy value of the output on the energy consumption side to the total exergy value of the input on the energy supply side, the exergy efficiency evaluation about energy efficiency are carried out, and the optimal dispatching operation model of exergy efficiency is proposed. Finally, the validity and rationality of the proposed method and model are verified by simulation examples. The proposed method comprehensively considers the two attributes of energy “quantity” and “quality” based on energy quality characteristics, and conducts integrated energy system coordinated optimization scheduling from the perspective of exergy efficiency, achieving high-quality utilization of energy, high-efficiency operation of the system, and promotion of new energy consumption.