Non-point source pollution(NPS) had deteriorated water quality in Miyun Reservoir watershed. GIS technology, ArcSWAT model, and statistics analysis were coupled to identify the zonation of NPS control in Chaohe river watershed, one main tributary in northeast of Miyun Reservoir watershed, with relative strong intensive agricultural activities. The results showed that annual average loads of TN and TP were 563.3t/a and 28.7t/a, respectively. The spatial distribution of NPS pollution load was greatly diverse with different precipitation and terrain in Chao river watershed. In high flow year, the agricultural land at higher elevation had the highest NPS pollution loads, whereas in the normal and low flow year, the agricultural land and livestock area also contribute the major pollution load; the fertilizer application amount was identified as the most important factor of TN and TP loss. Meanwhile, the slope length, soil type, land use, and slope degree were also more important factors; The content of organic P in soil may contribute to TP loss due to long term cultivation and overuse of fertilizer in Chaohe river watershed; Three zones for NPS control in Chaohe river watershed were divided as pollution control zone where the agricultural activities was intensive, pollution treatment zone where was livestock breeding area and villages, ecological restoration zone where was high soil erosion at higher elevation.