Abstract: The reasonable arrangement of water allocation time and discharge of each canals, realization of water allocation of large discharge and short time about irrigation canals system and reduction of water transportation loss in irrigation district management are pressing technological problems. Traditional method based on the two-level canal system, can not optimize water allocation marshaling of multilevel irrigation canal system. To solve the problems a new model based on the idea of decomposition and coordination is established. As to many restriction conditions and large searching space problem in the model, solution method based on self-adaptive genetic algorithm is designed，and comparison between the optimal water allocation and the traditional method shows that there are more advantages in the method of this paper than the traditional method. For example, it can analyze the model with multiple restriction conditions quickly and stably using the optimal water allocation program. The water in the lateral channels is allocated more reasonably, and the superior water flow is more uniform, and the total water transportation loss is the lowest. The water delivery scheduling problems of multilevel optimal irrigation canal system can be solved, which meet the requirement of irrigation management.