Vegetation rehabilitation is the key measures for maintaining the soil and water resources and restoring the ecological environment in mountain areas. To explore the impact of vegetation rehabilitation on annual runoff, Hongmenchuan watershed located in Miyun Reservoir of Beijing was selected as research object. Mann-Kendal Test, Hydrological analysis based on separation evaluation method, and Zhang (2001) model were applied to quantify the respective contribution of climatic change and forest change to annual runoff of the area from 1989 to 2009. The results indicated that the mean annual precipitation and of Hongmenchuan watershed showed a fluctuant decreasing but not remarkable trend from 1989 to 2009, while the runoff showed a significant decreasing trend. Combined with the results of cumulative runoff rate curve and independent sample t-test, the annual runoff had a significant decreasing trend with the change point occurred in 1998. Human activities were the strongest contributor to the reduction in mean annual streamflow of Hongmenchuan watershed, and the contribution rate reached 57%, while the remaining caused by climatic variations. Different types of human activities on the reduction in annual streamflow were quite different, for instance, the contribution rates of vegetation rehabilitation and construction on runoff was about 25.34%. In summary, compared with vegetation restoration, reduction in precipitation has a greater impact on the water yield. The results provide a theoretical reference for basin water resources management and land-use planning in Beijing Mountain areas.