Agricultural water shortage is serious and ecological environment becomes deteriorating continuously due to the reducing available Yellow River water resources and serious agricultural non-point source pollution in Hetao Irrigation District, Inner Mongolia. Based on these problems, the footprint concept was introduced into the multi-objective optimization model and multi-objectives decision evaluation model to allocate the limited water resources rationally. Taking Hetao Irrigation District as an example, the optimal planting structures of five main crops (wheat, corn, sunflowers, tomatoes and melons) were obtained considering the aspects of economy, society, resources and ecology. Meanwhile, multiple optimization schemes (multi-objective condition, single-objective condition and current condition) were evaluated and selected by integrating the FAHP model and TOPSIS model. Results showed that under the basic premise of food crop yield, reducing the planting area of wheat and corn, and increasing the cash crops (sunflowers, tomatoes and melons) were recommended. It can increase economic income, ensure social equity, improve irrigation water use efficiency and reduce the negative environmental effects simultaneously. Furthermore, the evaluation results showed that the multi-objective optimization scheme, taking into account the tradeoffs amongst economic, social, resources and environmental aspects, was better than both the single-objective condition and the current condition. The research result can provide theoretical decision support and promote sustainable development to Hetao Irrigation District and similar irrigation areas.