In recent years, the water resources conditions in the source area of the Yellow River have changed considerably, based on 58 years of runoff and meteorological data from 1961-2018, Mann-Kendall test and wavelet analysis were used to analyze the characteristics and influencing factors of these runoff changes. The results show that the runoff showed a non-significant decreasing trend as a whole by the rate of -0.63×108 m3/a, with a larger decrease in summer and autumn, but a smaller decrease in winter and spring; however, it presented a non-significant increasing trend both before and after 1990, and the increasing trend accelerated significantly after 1990, the latter was 3.09 times of the former. Meanwhile, the increasing high value area of precipitation overlapped with that of temperature after 1990, and precipitation was the most important factor affecting runoff changes. These findings indicate that the accelerated warming and humidification, as well as its spatial migration directly led to the accelerated melting of glaciers, which was also the reason for the rapid increase of runoff after 1990 in the source region of the Yellow River.