Abstract: In order to alleviate contradiction between supply and demand of Isatis indigotica planting water resources in Hexi Oasis, solve problem of extensive irrigation decision-making in irrigation process, and improve efficiency of irrigation water use, by referring to Jensen model, water balance equation, etc., according to environmental characteristics of drought and little rain in the Hexi Oasis and growth law of different water consumption intensity in each growth period of Isatis indigotica, an irrigation decision-making model of Isatis indigotica was constructed and genetic algorithm was used to solve reasonable allocation of limited water resources in Isatis indigotica irrigation．At the same time, considering constraints of irrigation water volume, effective precipitation, irrigation cost, yield and other factors in each growth period, under guidance of insufficient irrigation theory, genetic algorithm was used to optimize irrigation decision with existing Isatis indigotica planting data to achieve goal of water saving, high efficiency and high yield．Optimization results showed that slight water deficit of fleshy roots could significantly improve efficiency of irrigation water use, which was consistent with actual planting irrigation situation．