To analyze the changing trends and variation characteristics of the hydrological response of the main trunk and tributaries in the Yongding River Basin, a method for attributing variations in natural runoff was proposed, and a quantitatively attribution analysis of the changes in the hydrological response of the Yongding River Basin was conducted. Then the driving factors of the changes in the hydrological response were also explored. The results demonstrate that the annual natural runoff of the main trunk and tributaries in the Yongding River Basin shows a significant attenuation trend, and a sudden change occurred in the early 1980s. The hydrological response of the basin experiences significant structural changes before and after the sudden change. The contribution rate of climate change to the decline of natural runoff of the trunk and tributaries in the Yongding River is 10.9% to 24.5%, while the contribution rate of human activities is 75.5% to 89.1%. The uniformization distribution of precipitation time course, warming and drying climate, increased vegetation cover, and groundwater extraction are the main driving factors for changes in natural runoff and hydrological response in the Yongding River Basin.