Increasing the promotion and application of biofuel ethanol has been a national strategy in China, which in turn has affected changes in the raw material planting structure. This study analyzed the effects of agricultural land-use changes on water quality in a typical maize fuel ethanol raw material planting area. The results revealed that an increase in cultivated land and construction land would also increase the load of TN (total nitrogen) and TP (total phosphorus), while an expansion in forest land would reduce the load. As for crop structures, maize might have a remarkable positive effect on TN and TP, while rice and soybean performed in no significant manner. Furthermore, scenarios under the carbon neutralization policy and water pollution control were carried out to forecast the nonpoint source pollutants based on the quantitative relations coefficients. It was proven that maize planting was not suitable for vigorous fuel ethanol development. Reducing maize area in the Hulan River Basin was beneficial to reducing nonpoint source pollution. However, the area of maize should not be less than 187 km2, otherwise, the food security of the population in the basin would be threatened. Under the change in fuel ethanol policy, this study could provide scientific support for local agriculture land-use management in realizing the carbon neutralization vision and set a good example for the development of the fuel ethanol industry in other maize planting countries.