Quantitative analysis of the impact of precipitation and underlying surface changes on runoff is of great significance to water resources planning and management in river basins. Taking Manshuihe watershed, Beijing as the research object, the trend and abrupt change point of the annual precipitation and natural runoff series from 1956 to 2016 were analyzed, the relationship of double cumulative curve between annual precipitation and natural runoff was established based on data in the period of 1956-1979 which was before the runoff abrupt change, and the contribution rates of precipitation and underlying surface changes on natural runoff were identified for different period compared with the base period 1956-1979. The results showed that the direct effect of human activities such as water consumption, regulation and storage of water conservancy project after 2000 year decreased. The effect of precipitation on runoff reduction for 1990-1999 period was 63.9%, greater than that of underlying surface change. The effect of underlying surface change on runoff reduction for 1980-1989,2000-2009 and 2010-2016 periods was greater than that of precipitation, the contribution rates of precipitation and underlying surface changes on runoff reduction were respectively 44.9% and 55.1% for 1980-1989, 47.9% and 52.1% for 2000-2009, 44.5% and 55.5% for 2010-2016.