<p>Accurate identification of key areas of agricultural non-point source pollution is essential for evaluating the effectiveness of environmental policies. However, existing research often lacks long-term systematic assessments and accurate delineation of priority regions. This study aims to examine seven representative flue-cured tobacco-producing areas in Yunnan Province, China, analyze the spatiotemporal evolution of nitrogen and phosphorus grey water footprints from 2010 to 2022, and identify critical source areas of agricultural non-point source pollution. To address the lack of municipal-level fertilizer-use data, a Fertilization Intensity Weighting Method was developed to downscale provincial fertilizer data to the prefectural level, providing methodological support for crop-specific grey water footprint assessment. The results show that: (1) The grey water footprint of phosphate fertilizer greatly exceeds that of nitrogen fertilizer and is therefore the primary contributor in flue-cured tobacco cultivation. This indicates that phosphorus pollution is the dominant environmental pressure. (2) During the study period, both nitrogen and phosphorus grey water footprints, as well as their intensities, showed an overall declining trend, with peak values around 2012. (3) Spatially, the distribution follows a pattern of “higher in the east than in the west and higher in the north than in the south.” Qujing City and Baoshan City are identified as the regions most severely affected by non-point source pollution. The findings provide a scientific basis for identifying agricultural pollution pressure zones and for developing differentiated strategies for green cultivation and water pollution control.</p>