Since the 1950s, China has implemented numerous soil and water conservation measures to control severe soil erosion in the Liu River Basin (LRB). While these measures have protected the upstream soil and water ecological environment, they have led to a sharp reduction in the downstream flow and the deterioration of the river ecological environment. Therefore, it is important to evaluate the impact of soil and water conservation measures on hydrological processes to assess long-term runoff changes. Using hydrological models and sensitivity analyses based on the Budyko hypothesis, this study quantitatively evaluated the effects of climate change, direct water withdrawal, and soil and water conservation measures on runoff in the LRB during different periods. The runoff series was divided into a baseline period (1956–1969) and two altered periods, period 1 (1970–1999) and period 2 (2000–2020). Human activities were the main cause of the decrease in runoff during the altered periods, contributing 86.3% (− 29.61 mm), while the contribution of climate change was only 13.7% (− 4.7 mm). The impact of climate change manifests as a decrease in flood volume caused by a reduction in precipitation during the flood season. Analysis of two flood cases indicated a 66–84% reduction in basin runoff capacity due to soil and water conservation measures in the upstream area. Soil and water conservation measures reduced the peak flow and total flood volume in the upstream runoff area by 77.98 and 55.16%, respectively, even with nearly double the precipitation. The runoff coefficient in the reservoir area without soil and water conservation measures was four times that in the conservation area. These results contribute to the re-evaluation of the soil and water conservation hydrological effects and provide important guidance for water resource planning and water conservation policy formulation in the LRB.