The loss of nitrogen and phosphorus via non-point source (NPS) pollution in the Chaobai river watershed has become the main pollution sources of river waters in the Miyun reservoir area in the past decades. Climatic conditions and human activities directly affect changes of runoff. In addition, land use types are closely related to NPS pollution. Climate change and human activities can potentially lead to changes in runoff and can significantly impact the regional hydrology and future availability of water resources. Researches showed that NPS pollution has become an important source affecting the quality of the Miyun reservoir water environment. Therefore, exploring the impact of land use change on NPS pollution under different climate scenarios has important practical implications for control non-point source pollution in this area. In this study, Miyun reservoir watershed was used as a study area to determine the response of non-point source pollution to land use change under different climate scenarios. An integrated model system was developed which included three parts, the Soil and Water Assessment Tool (SWAT) as the hydrological and non-point source pollution estimator; the Canonical Correspondence Analysis (CCA), and Path Analysis to explore the relationship between land use change and non-point source pollution loads. The statistical downscaling model was conducted to generate the different climate scenarios for discussing the impact on hydrological process and non-point source pollution losses. The results showed that SWAT model was suitable for the study area. Total nitrogen (TN) and total phosphorus (TP) loads decreased with the rainfall during 1995 to 2005, indicating that the rainfall was an important factor on the temporal variability of pollution loads. The spatial distribution of TN and TP loads were significantly affected by the comprehensive influence of rainfall and land use. The high-risk areas were mainly located in Chicheng, Chongli, and Fengning county. There was a significant correlation (P<0.05) between NPS pollution loads and landscape characteristics in the upper watershed of Miyun reservoir. Correspondence Analysis (CCA) and Path Analysis indicated that landscape variables can explain 56.3% variation of TN and TP loads. For landscape level, the fragmentation metrics, and shape metrics were the main pattern indices effectively affecting the variation of nutrient losses. For patch-class level, landscape metrics that affected the spatial variation of pollution process varied with land use types. The result of path analysis suggested that the proportion of arable land and forest land area, patch density, and shape index were the main pattern indices effectively affecting the nutrient pollution process. The interpretation capacity of proportion of arable land and shape index to TN and TP loads was greater than the other indicators. The relationship was closely associated with the spatial scale. With the spatial scales increased, the interpretation capacity of landscape variables reduced. Cumulative variances of the first grade protection zones are the highest in CCA ordination analysis, which reached 62.9%, indicating that the area around the reservoir area should be highly valued for the prevention and treatment of NPS pollution. As a result of this work, prioritized areas and the relationship between nutrients load and land use pattern can be used as information for implementation of conservation practices in the Miyun reservoir watershed.