The agricultural economic loss of the river ecological base flow protection directly determines government decision-making on the protection of the ecological base flow, and provides the quantitative basis to remain a reasonable level of the ecological river base flow protection. Based on the farmland ecosystem services value loss caused by the river ecological base flow protection grain loss, we proposed a calculation method to compute the farmland ecosystem services value loss based on the river ecological base flow protection. The change rule of service value loss of farmland ecosystem was discussed and the way of dealing with value loss was analyzed. The effect of grain market value on the loss of service value of farmland ecosystem service was analyzed. The results show that runoff is the basis to calculate farmland ecosystem services value loss, and the annual distribution influences farmland ecosystem services value loss. We can deal with the economic loss based on the river ecological base flow protection by the water right trading method and the agricultural ecological compensation method, which can promote the coordinated development of the agriculture and the river ecological basic flow, and food market fluctuation also cause farmland ecosystem services value loss change.