Abstract: The optimal allocation of water resources in irrigation areas is one of the important control methods to realize the sustainable utilization of agricultural water resources. However, two great challenges remain at present, including the water resources shortage and non-point source pollution. Therefore, it is highly urgent to optimize management practices and then reasonably allocate agricultural water resources during agricultural production. It is also of great practical significance to consider the multi-folded impacts of inadequate irrigation on economic benefits, crop quality, and environmental soundness. Among them, insufficient irrigation is an effective management measure to efficiently use irrigation water for the high quality and yield of crop production. Previous modeling of water resource allocation cannot fully reflect the economic and crop yield parameters in crop production and irrigation water resources system, the irrigation quantity on crop quality, the pollutant leaching, and the impacts of insufficient irrigation on the economy, quality and environment. In this study, an economic-quality-environment multi-objective mixed-integer programming model was established for the Hetao Irrigation District using insufficient irrigation and grey water footprint. An uncertainty quantity was also introduced into the water-quality model for the decision-making schemes under different preference levels using Analytic Hierarchy Process (AHP). The decision plans were then generated to allocate the irrigation water during the crop growth period under three scenarios, indicating different preferences over economy, quality, and environment. The results showed that the irrigation degree of preferred environmental goals was mainly 33%, followed by 66%, indicating a greater degree of deficit irrigation. The irrigation level of preferred economic goals was mostly 100%, indicating a smaller degree of deficit irrigation. A preference for the quality goals fell between the two levels. The developed model for the tomato and lemon was compared with those that only included the single target of economy, quality, and environment, showing more balanced plans with higher comprehensive benefits. Among them, the quality index of tomato quality-economy-environment multi-objective model was 8.7, the economic benefit was 21.3×108 yuan, the grey water footprint was 1.62×104 m3, and the amount of irrigation water was 3.51×107 m3. The quality index of melon quality-economy-environment multi-objective model was 25.3, 32.7, the economic benefit was 9.2×108, 24.8×108 yuan, the grey water footprints was 1.94×104, 3.15×104 m3, and the amount of irrigation water was 6.32×107, 7.62×107 m3. Consequently, the simulation increased the comprehensive benefits of crop production for the less grey water footprint, in order to promote the efficient and green utilization of irrigation water resources. An optimal solution was also proposed to adjust the crop planting structure and irrigation water allocation. The finding can also provide strong support to allocate the irrigation water under insufficient irrigation in the sustainable management of irrigation areas, without the loss of generality across the world.