The source regions of the Yangtze River (SRYZ) and the Yellow River (SRYR) are sensitive areas of global climate change. Hence, determining the variation characteristics of the runoff and the main influencing factors in this region would be of great significance. In this study, different methods were used to quantify the contributions of climate change and other environmental factors to the runoff variation in the two regions, and the similarities and differences in the driving mechanisms of runoff change in the two regions were explored further. First, the change characteristics of precipitation, potential evapotranspiration, and runoff were analyzed through the observational data of the basin. Then, considering the non-linearity and non-stationarity of the runoff series, a heuristic segmentation algorithm method was used to divide the entire study period into natural and impacted periods. Finally, the effects of climate change and other environmental factors on runoff variation in two regions were evaluated comprehensively using three methods, including the improved double mass curve (IDMC), the slope change ratio of cumulative quantity (SCRCQ), and the Budyko-based elasticity (BBE). Results indicated that the annual precipitation and potential evapotranspiration increased during the study period in the two regions. However, the runoff increased in the SRYZ and decreased in the SRYR. The intra-annual distribution of the runoff in the SRYZ was unimodal during the natural period and bimodal in the SRYR. The mutation test indicated that the change points of annual runoff series in the SRYZ and SRYR occurred in 2004 and 1989, respectively. The attribution analysis methods yielded similar results that climate change had the greatest effect on the runoff variation in the SRYZ, with a contribution of 59.6%~104.6%, and precipitation contributed 65.3%~109.6% of the increase in runoff. In contrast, the runoff variation in the SRYR was mainly controlled by other environmental factors such as permafrost degradation, land desertification, and human water consumption, which contributed 83.7%~96.5% of the decrease in the runoff. The results are meaningful for improving the efficiency of water resources utilization in the SRYZ and SRYR.