The combined operation of large-scale off-grid wind turbines and energy-intensive seawater desalination equipments will be one of the directions of the cleaner freshwater producing technology in the future. Based on load characteristics of seawater desalination devices and operating characteristics of wind power, the operation modes and control strategies of isolated microgrid with wind power, energy storage and seawater desalination equipments are discussed firstly. On this basis, the unit outputs and the probability distributions of wind power fluctuation are calculated according to historical data of wind speed, and then the capacity configuration of wind power, energy storage and seawater desalination devices and the coordinated control strategy of isolated microgrid to enhance the economical efficiency and stability of the system are proposed, respectively. Finally, a digital-analog simulation platform is built based on PXI+cRIO. The real-time simulation result for various operating modes of this isolated microgrid system verifies the feasibility of the proposed control strategies.