The change in river flows at the basin scale reflects the combined influences of changes in various environmental factors associated with climatic and underlying surface properties. Distinguishing the relative contribution of each of these factors to runoff change is critical for sustainable water resource management, but it is also challenging. The headstream region of the Yangtze River, known as “China’s Water Tower”, has undergone a significant runoff change over the past decades. However, the relative contribution of environmental factors to runoff change is still unclear. Here, we designed a series of detrending experiments based on a grid-based hydrological model to quantify the combined influences of multiple environmental factors on runoff change and the relative contribution of an individual factor to runoff change. The results indicate that changes in climate and vegetation significantly increased water yield in the study basin over the past three decades, and the increase in water yield primarily came from the contribution from the upstream of the basin. On the basin scale, the change in precipitation dominated the runoff change that contributed up to 113.2% of the runoff change, followed by the wind speed change with a contribution rate of −15.1%. Other factors, including changes in temperature, relative humidity, sunshine duration (as a surrogate for net radiation), and albedo (as a surrogate for vegetation) had limited effects on runoff change, and the contribution rate of these factors to runoff change ranged from −5% to 5%. On spatial patterns, the influences of changes in some environmental factors on runoff changes were affected by elevation, particularly for temperature. The rising temperature had mixed effects on runoff change, which generally increased water yield at high altitudes of the basin but decreased water yield at low altitudes of the basin.