Abstract: Background To evaluate the characteristics of agricultural non-point source (NPS) pollution in small watersheds upstream of the Danjiangkou Reservoir, identify key pollution sources, and support targeted pollution control strategies, this study focused on the Yahe River small watershed in Xichuan County, Nanyang City, Henan Province.Methods Based on field survey data, we applied the inventory analysis method and the equivalent pollution load method to estimate the nitrogen and phosphorus pollution loads from agricultural non-point sources. We further analyzed the emission structure, spatial distribution, and contribution rates of different pollution sources.Results The results show that: (1) Chemical fertilizer application was the primary source of nitrogen and phosphorus pollution, with an equivalent pollution load of 30,661.6 × 10³ m³, accounting for 68.08% of the total load. This was followed by livestock farming (7,425.1 × 10³ m³, 16.48%) and rural domestic pollution (6,501.8 × 10³ m³, 14.44%). Agricultural solid waste made a minimal contribution, representing only 1% of the total load. (2) The intensity of NPS pollution showed a clear increasing trend from upstream to downstream. The upstream sub-basins (3 and 4) contributed 12.52% of the total pollution load, the midstream sub-basins (2 and 5) contributed 32.14%, while the downstream sub-basins (0 and 1), with the most intensive human activities, contributed 55.34%, identifying them as the critical areas for pollution control.Conclusions This study provides fundamental data for understanding the formation mechanisms of agricultural NPS pollution in small watersheds of the Danjiangkou Reservoir area, and offers a scientific basis for formulating targeted integrated watershed management strategies and best management practices in water conservation zones.