Due to the rising tensions surrounding the energy industry in response to the depletion of non-renewable energy sources and pollution of the environment, it is especially important to improve the energy utilization rate of integrated energy systems (IESs). Exergy is an important index to measure energy quality. Therefore, this paper proposes an IES operation optimization method based on exergy analysis and an adaptive genetic algorithm. First, based on the energy network theory, a unified expression of the exergy transfer process is given, and the energy level factor is introduced to evaluate the energy quality. Second, the steady-state expression of different forms of exergy in the energy transfer line is given. Third, the exergy economic model of the IES is established by combining exergy analysis, and the solution process of the adaptive genetic algorithm is given. Finally, the operation optimization simulation and analysis of an IES in Bali are carried out to verify the effectiveness of the exergy analysis method and feasibility of the simulation method.