Urbanization has been responsible for the loss of cropland worldwide, especially in China. Since this trend is expected to continue in the near future, China has implemented the strictest cropland protection policies in the world, to guarantee its national food security. However, the negative impact of cropland protection policies on ecosystem services has always been ignored. In this paper, we used LANDSCAPE (Land System Cellular Automata model for Potential Effects) model to assess the ecological lands loss under different scenarios in Wuhan, China during S2010-2020. Our scenarios differ in whether or not the cropland protection policy is imposed. Then, the InVEST (Integrated Valuation of Ecosystem Services and Tradeoffs) model was used to calculate the amount of nutrient export under two different scenarios and to analyze the mechanism of impact of Cropland Balance Policy on water purification. Results show that the scenarios with strict cropland protection (CP) will lead to more losses of ecological lands compared with scenarios without cropland protection (NCP). Besides, the nitrogen export in the CP scenario is average 8.6% higher than the NCP scenario, which indicates that the Cropland Balance Policy has a negative impact on water purification. The nitrogen export is transported mainly by subsurface, which is 1.73 times higher than the surface averaged over the two scenarios. Accordingly, this study proposed that reasonable land use planning, and lowering the nutrient delivery ratio would be more beneficial to the ecosystem service of water purification.