In arid-semiarid regions, understanding the mechanisms by which vegetation change and climate change affect the regional water balance is important for the development of effective measures and for guiding vegetation restoration and adapting to climate change. In this study, we utilize the Budyko equation and dual-source evapotranspiration models to assess the impacts of vegetation change and climate change on the runoff in China's Yellow River Basin (YRB). The aims of the study are as follows: (1) Apply a well-formulated Budyko framework-dual-source evapotranspiration model to explore the eco-hydrological controls of the regional water balance. (2) Precisely assess the contribution of vegetation change, precipitation change, temperature change, wind speed change, the relative humidity change, and radiation change to the decreased runoff. The results indicated that vegetation change was the dominant factor affecting the reduction of runoff in the upper reaches above Lanzhou, Toudaoguai, Longmen, Sanmenxia, and Huayuankou, and the contributions were −80.4%, −58.4%, −52.5%, −46.9%, −39.7%, and −41.6% respectively. In Lanzhou, Taodaoguai, Longmen, and Sanmenxia, the precipitation change was the second affecting factor, and the contributions were −20.8%, −31.6%, −30.0%, and −35.2%, respectively. In Huayuankou and Lijin, the relative humidity change was the second affecting factor, and the contributions were –26.8% and −35.0%, respectively. (3) As the vegetation coverage or the leaf area index (LAI) increased, the runoff decreased linearly.