According to the agricultural irrigation water shortage in dry season caused by the ecological base flow security, it is necessary to study its effect on irrigation district and ecological compensation so as to promote the sustainable development of base flow protection and improvement. First, the possible impact of irrigation water shortage should be qualitatively analyzed. Next, the amount of irrigation water in irrigation district caused by different base flow security proposals should be clearly determined. And then the crop production losses caused by irrigation water shortage should be estimated by the water production function model, and also the amount of ecological compensation for irrigation areas should be determined. Taking Shaanxi section of Weihe River as an example, the water shortage caused by three base flow security programs was analyzed and calculated in the irrigation area. The results showed that the ecological compensation amounts of winter wheat in Baoji gorge Yuanshang irrigation area, Yuanxia irrigation area and Jiaokou irrigation area were 28.003 million yuan, 323.926 million yuan and 988.180 million yuan under three ecological base flow security schemes respectively.