Yingke Irrigation District (YID) is one of the typical irrigation district in the middle oasis of Heihe River Basin. With the low agricultural water use efficiency, the contradiction between the supply and requirement of agricultural water use is outstanding. The maize for seed is the main crop in YID, and it is of great significance to study the optimized irrigation system for the production of seed maize for the sustainable development of agricultural water in the region. In this paper, the irrigation system of maize for seed was optimized based on the AquaGIS model and the spatial variability of soil texture in YID, and the best irrigation system suitable for the actual condition in YID were proposed. Through the optimization of irrigation system, the evapotranspiration of maize for seed in YID reduced from 36 mm to 53 mm, the water productivity (WPET) increased by 5%, and the irrigation water productivity (WPl) increased by 25%-48%, which greatly improved the agricultural water use efficiency of the irrigation area. At the same time, the irrigation system of different hydrological years in the irrigation district was optimized. Comprehensively comparing the WPET, WPl and yield of maize for seed, the optimal irrigation system for different hydrological years was proposed, that is, three times for wet years, four times for normal years and five times for drought years, providing theoretical guidance for high efficiency water saving irrigation in YID.