In order to scientifically coordinate the contradiction between agricultural water use and ecological base flow in water shortage areas, and to promot the ecological base flow guarantee work, this paper determines the amount of agricultural losses under different levels of protection from the perspective of the impacted agriculture from ensuring the ecological base flow. Taking the Baoji section of the Weihe River as an example, the agricultural output value loss and yield loss in Baojixia Irrigation District were calculated quantitatively when the ecological base flow regulation value was between 5 and 10 m3/s, and the change of the protection rates before and after the ecological base flow protection was analyzed. The results showed that when the ecological base flow regulation value was between 5 and 10 m3/s, the agricultural output value loss were 1.04×108-2.54×108 yuan, 2.99×108-4.06×108 yuan and 4.78×108 - 6.61×108 yuan, respectively in normal year, dry year and extremely dry year. The river ecological base flow protection rate had significantly improved, when the diversion for agricultural irrigation reduced.