In view of present administration situation of irrigated areas in our country, develop a precision and intelligent irrigation decision support system (DSS) with simple, convenient and easy to apply is indispensable. Based on genetic algorithm (GA) with two layers, the optimize pattern was adopted by the system. The first layer is to achieve the optimization of water allocation of the unitary crop in the different growing periods. The second layer is to achieve the optimization of water allocation of many kinds of crops and it was combined with the expert system. This composition effectively averted the limitations of GA when it was used to resolve the problems of part searching. MapInfo was adopted in the system as the communicate interface of user and PC and it made the decision of strategic importance easy to see and the system easy to operate. In running structure, the DSS consisted of five modules: the data acquisition module, the information management module, the simulation module of crop water allocation, the optimize module with GA and the display module of irrigated areas information.