The DMCs indicate that human activities clearly impact runoff change. The variations in hydrological processes were not only affected by precipitation, but also by human activities in the catchment. To quantitatively analyze the impacts of human activities and precipitation variations on runoff change, we use the period less affected by human activities (before the breakpoint) as a reference period based on the characteristics of the DMCs. The reference period of the Lanzhou and Toudaoguai sections is 1956 to 1992. The reference period is 1956 to 1970 for the Huayuankou and Lijin sections. The period after the breakpoint is the affected period, in which human activities impact runoff variations. The regression equations for the reference period were used to represent the effects of precipitation variations on the runoff variables. By extending the regression equations between observed runoff and precipitation during the reference period to the precipitation in the affected period, runoff variations due to precipitation variations can be estimated. By subtracting the observed values of runoff variables from estimated values based on precipitation, the changes caused by human activities can be further estimated. The estimated contributions of precipitation variations and human activities to runoff changes in different sections are summarized in Table 5 for the affected periods. Runoff in the Lanzhou section decreased by 18.70% compared with the reference period. Additionally, the contributions of human activities and precipitation variations are 74.87% and 25.13%, respectively. In the Toudaoguai section, the runoff is more negative compared with the reference period. The impacts of human activities and precipitation are 82.20% and 17.80%, respectively. In the middle reaches of the YRB (Huayuankou section), runoff consistently decreased throughout the entire period after 1969. Human activities played a role in decreasing runoff, with contributions of 80.36% and 80.63% in 1970–1989 and 1990–2010, respectively. In the lower reaches, the impact of human activities gradually increased, dominating the runoff change with contributions of 83.98% and 88.71% in the two affected periods. These results provide the quantitative contributions of human activities and precipitation to the runoff change based on the reference period. Generally, human activities increasingly contribute to temporal and spatial runoff change in the YRB.