The integrated energy system (IES) optimal scheduling under the comprehensive flexible operation mode of pumping storage is considered. This system is conducive to the promotion of the accommodation of wind and solar energy and can meet the water, electricity and heat needs of coastal areas far away from the energy center. In this study, the joint dispatch between double pumped storage power stations is used to accommodate wind and solar energy better and smooth their fluctuations on the grid. Through the scheduling of water between the high and low reservoirs of double pumped storage power stations and the reservoir of the seawater desalination plant, the impact of storage capacity constraints on pumped storage power plants is reduced. Moreover, the objective function to build the IES optimization scheduling model is to achieve minimum economic cost. The results reveal that the integrated energy system accommodates all wind energy and solar energy. As such, the system increases the average working time of the pumped storage unit by 1.9 hours and reduces the economic cost by 31.50%. Based on the simulation results, the model can enhance the accommodation capability of wind energy and solar energy and improve the system economy.