The energy flow in energy supply system has become further complicated due to the addition of multiple clean primary energy and the integration of energy storage technique, which gives rise to the main challenges for integrated energy system (IES) designing on how the IES coordinates the start and stop or varying load operation of multiple equipment so as to maximize the energy conservation and emission reduction and economic benefits. In this paper, with the integration of multiple primary energy utilization technologies and combination of various energy conversions and storage equipment, a superstructure model of IES with multiple complementary energy is established by the way of gradually decomposing and modeling, taking the optimal annual total cost (ATC), primary energy consumption (PEC), and CO2 emission (CE) as the objective function, which can harmonize the energy supply and demand restrictions and the relations of energy flow in the subsystems of energy production system (EPS), energy conversion system (ECS), and energy storage system (ESS). The scientific installed capacity and optimum operation strategy can be solved by this model, which is applied for the designing of integrated energy supply scheme for one certain park. The result shows that the model is both suitable for the energy supply scheme research and the scientific and rational planning and designing for integrated energy of IES with multiple complementary energy.