Agricultural Cultivation Structure in Arid Areas Based on Water–Carbon Nexus—Taking the Middle Reaches of the Heihe River as an Example

China faces challenges of food security and sustainable agricultural production. However, current studies rarely address the spatial distribution patterns of water consumption and carbon emissions. We studied the irrigation water use efficiency and carbon emission differences of crops in arid areas and their spatial distribution using wheat and maize, two major food crops in the middle reaches of the Heihe River, as examples. Furthermore, we have optimized low-carbon cropping of crops under the multiple objectives of water conservation and economic development. The results show that: (1) The carbon emissions per unit of water consumption for maize are 0.03 × 10 −6 t mm −1 and 0.49 × 10 −6 t mm −1 for wheat. Irrigation water consumption per unit yield is 515.6 mm t −1 for maize and 426.7 mm t −1 for wheat. (2) The spatial distribution patterns of irrigation water consumption were opposites for maize and wheat. The former has lower irrigation water consumption in the planting area upstream of the Heihe River and higher in the lower reaches. In contrast, the pattern of wheat irrigation is the opposite. (3) After optimizing the cropping mix for both crops, the area planted with wheat should be reduced to 59% of the current size, while maize should be expanded to 104%. The results of the research hold immense importance in guiding the future grain crop planting patterns for water-saving agriculture and low-carbon agriculture development in arid zones worldwide, aligning with the United Nations’ Sustainable Development Goals.