Water erosion causes reduced farmland productivity, and with a longer period of cultivation, agricultural productivity becomes increasingly vulnerable. The vulnerability of farmland productivity needs assessment due to long-term water erosion. The key to quantitative assessment is to propose a quantitative method with water loss scenarios to calculate productivity losses due to long-term water erosion. This study uses the agricultural policy environmental extender (APEX) model and the global hydrological watershed unit and selects the Huaihe River watershed as a case study to describe the methodology. An erosion-variable control method considering soil and water conservation measure scenarios was used to study the relationship between long-term erosion and productivity losses and to fit with 3D surface (to come up with three elements, which are time, the cumulative amount of water erosion and productivity losses) to measure long-term water erosion. Results showed that: (1) the 3D surfaces fit significantly well; fitting by the 3D surface can more accurately reflect the impact of long-term water erosion on productivity than fitting by the 2D curve (to come up with two elements, which are water erosion and productivity losses); (2) the cumulative loss surface can reflect differences in productivity loss caused by long-term water erosion.