Miyun Reservoir is the main source of drinking water for Beijing. However, it is increasingly threatened by losses of nitrogen and phosphorus from slope farmland in the drinking water source protection catchment. A contour hedgerow intercropping system of forage mulberry (Morus multicaulis Perr.) and medicinal plant was planted to control and mitigate the non-point source contaminants in the catchment. Free-range Beijing Fatty Chickens were raised in the intercropping areas (free-range mode) to feed on mulberry additives in the adjacent areas (feeding mode). Topsoil samples from the two modes were collected for determination of organic matter, nitrogen, phosphorus and potassium contents, and mulberry samples from the free-range mode and its control were collected for determination of nitrogen (N), phosphorus (P) and potassium (K) contents in the plant. The results showed that compared with the controls, the soil organic matter content(OM), total nitrogen(TN), available N, P and K, and nitrate of the two mode areas increased significantly, which promoted the growth of the mulberry and medicinal plant and the nutrient uptake; the soil organic matter, TN and total phosphorus(TP) were greater in the feeding and free-range mode with high density of 60 and low density of 20 chickens per mu, respectively, than those in the free-range mode. However, compared with the upper parts of the slope farmland in the free-range chickens with high density, the soil available N, P and K at the lower parts of the slope farmland were increased by 20.3%, 71.9% and 21.9%, respectively. It suggests that the soil nutrient accumulation could be related to the feeding density and runoff. The nitrogen and phosphorus loads from chicken manure in the feeding mode were 189kg/hm² and 84.8kg/hm², respectively, which exceeded the EU (European Union) limits of 170kg N/hm² and 80kg P₂O₅/ hm², respectively; it could lead to high N and P losses to the Reservoir. The N and P loads in the free-range mode were 75.6kg/hm² and 33.9kg/hm², respectively, much less than the environmental limits, thus resulting in less risk of nutrient losses. Therefore, the decomposition and mineralization of chicken manure in the contour hedgerow intercropping system of forage mulberry and medicinal plant can supply nutrients to the intercropping plants, on the other hand, it can effectively prevent the loss of organic matter and nitrogen and phosphorus, and provide feed to free-range chickens. These results suggest that the intercropping system of forage mulberry/medicinal plant/ low-density free-range chicken is an effective ecological mode for controlling and mitigating water contamination by agricultural non-point source pollution in the catchment.