The accumulative anomaly analysis method was used to analyze the changing trends of the precipitation and runoff from 1990 to 2016 in the upper Sanchahe River Basin, the water source area of the Qianzhong Hydraulic Project. Two mutational points in the process of precipitation change in the upper Sanchahe River Basin in 2001 and 2013 were detected. However, there was only one abrupt point in 2001 in the process of runoff change. The slope change ratio of cumulative quantity was adopted to estimate the contribution rates of the precipitation and human activities to the runoff change in different time periods. The results showed: taking 1990-2001 as the base period, the contribution of precipitation and human activities to the decreased runoff were 59.37% and 40.63% in 2002-2013, while the contribution rates of precipitation and human activities to the reduction of runoff from 2014 to 2016 were 50.82% and 49.18%, respectively. This study have shown that precipitation was the main influencing factor to runoff change in the upper Sanchahe River Basin, and the influence of human activities to runoff change was increasing.