Assessing the characteristics of runoff changes and quantifying the contribution of influencing factors to runoff changes are crucial for water resources management and sustainable development in the source region of the Yellow River (SRYR). The intra-annual distribution of runoff depicted a double-peak effect. The first runoff peak in July was primarily influenced by precipitation, which did not completely flow after falling to the ground. However, some water was stored in the active layer of permafrost and released in September resulting in the second runoff peak. The contributions of precipitation and temperature to the runoff changes were 74.2% and 25.8%, respectively. The runoff peaks advanced by 15 and 6 days for the first and second peaks, respectively, owing to the influence of the cryosphere change. Principal component analysis revealed that the contributions of climate change and human activity to runoff fluctuations were 72.9% and 27.1%, respectively, during 1961-2018, indicating that hydrological processes were mainly influenced by climate change in the SRYR. The combined effect of climate change created a warm and dry trend after 1990, indicating a spatial distribution of wetness in the northwest and aridity in the southeast of the SRYR.