[Objective] To grasp the situation of agricultural non-point source pollution in Danjiangkou reservoir catchment areas in He'nan Province, and to prove the reliability of the fractal theory calculation results.[Methods] The fractal theory was applied to estimate the loss of total nitrogen(TN) and total phosphorus(TP) in the Danjiangkou reservoir region of He'nan Province in 2013. The estimated values were compared with the ones from output coefficient method.[Results] Pollutants loss was given priority to with nitrogen in the area, the TN loss was 7.16 times of TP loss. The livestock farming contributed the largest amount of loss, accounting for 69.93% of the total loss. The second was the loss from farmland fertilizer, taking up 21.99% of the total one. The pollutant yield of Guanhe River was the most, followed by Danjiang River, Qihe River and Taohe River. The pollutant erosion intensity had a rank as Taohe River > Guanhe River > Danhe River > Qihe River. The significant paired T test(<0.1) showed that the pollutant total amounts calculated by fractal method was coincided with the ones by output coefficient method, which indicated the former could reflect the actual situation more than that of the latter.[Conclusions] Fractal method is feasible to estimate logical agricultural non-point source pollution. It is time to strengthen management of livestock manure and chemical fertilizer to ensure the water quality of Danjiangkou Reservoir.