Many islands are far away from areas where power-grid arrives at difficultly in our country. To solve the problems of using electric and of using freshwater, hybrid wind pumped-storage desalination system was brought forward. Intelligent control of hybrid system was studied. The hardware flat of control system was built. The intelligent control strategy was put forward. Using VC#2008 visual interactive main control platform was established, which integrates data collection, data examination, control, data post-processing, data report-forms, data mimeograph and so on. By use of the control system hybrid wind pumped-storage desalination system can be monitored real time. According to dealing with real-time data the system's operating state can be estimated, then hybrid system can be intelligently dispatched, which assures high-electiveness and reliability of operation of hybrid system. The system is built in islands, which solves the problems of using electric and of using freshwater by use of local abundant wind source. By use of intelligent control system, the self-service on duty could be come true.