Crop production is expected to increase by more than 50% to meet the demand of population growth in China in 2050 (FAO, 2017). Crop production in North China largely depends on irrigation, which is mainly from groundwater in Northwest China. Over-extraction of groundwater is decreasing groundwater levels, and threatening the fragile ecological systems of arid regions. How groundwater levels will change in order to meet the irrigation water requirement in Northwest China has not been extensively investigated to evaluate sustainability of agriculture and the cost to maintain groundwater levels. Here, we examine the dynamic relations between groundwater levels and the amount of irrigation water, by employing the Variable Infiltration Capacity model and an irrigation scheme, for the last three decades in Heihe River basin of China. The results show that on the average about 1.86 m decline of groundwater is attributable to the irrigation water consumption for the farmland area in Heihe River over the past three decades. In the scenario of ceasing irrigation activities, the groundwater level will be prevented to further decline about 3.06±0.4m under the future climate scenarios till 2050, but at the cost of crop production valued 64.2±8.4 billion CNY. Effective water-saving measures and strategies are expected to adopt to maintain both groundwater levels and agricultural productivity for the coming decades.