This study estimates the total nitrogen (TN), total phosphorus (TP), and chemical oxygen demand (COD) emissions from agricultural non-point source pollution in the lower reaches of the Qinhe River from 2001 to 2021 using the pollution coefficient method. The results reveal that TN emissions decreased gradually, while TP and COD emissions initially increased before decreasing. Livestock and planting accounted for over 50% of TN, TP, and COD emissions, with COD being the most dominant pollutant (91.7%). Livestock and poultry farming, along with agricultural activities, were identified as the primary sources of TN and TP, while livestock farming and rural living contributed most to COD emissions. Spatially, Mengzhou City and Wuzhi County are the most polluted areas, highlighting the need for enhanced pollution control measures. Effective strategies include optimizing breeding layouts, integrating farming and livestock practices, enforcing stricter livestock scale and wastewater management controls, and providing practical and feasible strategies for preventing and controlling agricultural non-point source pollution in the lower reaches of the Qinhe River.