The integrated energy system is an important development direction for achieving energy transformation in the context of the low-carbon development era, and an integrated energy system that uses renewable energy can reduce carbon emissions and improve energy utilization efficiency. The electric power network and the natural gas network are important transmission carriers in the energy field, so the coupling relationship between them has been of wide concern. This paper establishes an integrated energy system considering electricity, gas, heat and hydrogen loads; takes each subject in the integrated energy system as the research object; analyses the economic returns of each subject under different operation modes; applies the Shapley value method for benefit allocation; and quantifies the contribution value of the subject to the alliance through different influencing factors to revise the benefit allocation value. Compared with the independent mode, the overall benefits of the integrated energy system increase in the cooperative mode and the benefits of all subjects increase. Due to the different characteristics of different subjects in terms of environmental benefits, collaborative innovation and risk sharing, the benefit allocation is reduced for new-energy subjects and increased for power-to-gas subjects and combined heat and power generation units after revising the benefit allocation, to improve the matching degree between the contribution level and the benefit allocation under the premise of increased profit for each subject. The cooperative mode effectively enhances the economic benefits of the system as a whole and individually, and provides a useful reference for the allocation of benefits of integrated energy systems. The analysis shows that the revised benefit distribution under the cooperative model increases by 3.86%, 4.08% and 3.13% for power-to-gas subjects, combined heat and power generation units, and new-energy units, respectively, compared with the independent function model.