The precipitation in the Zoige Plateau has decreased slightly and the evaporation has continuously risen, which reduced the water storage capacity of the Zoige Plateau continuously and led to the reduction of Zoige wetland area and decreased water resources supply into the upper Yellow River. The meteorological data of Hongyuan, Zoige and Maqu Counties and the runoff of seven hydrological stations in 1981-2011 were used to interpolate to obtain the completed the data series. The response relation between runoff change and climate factors was obtained, and the change of water storage in this region was calculated. The results show that the mean annual water supply of the Zoige Plateau into the upper Yellow River was(67.08±0.149)×108 m3, and decreased at a rate of 48×108 m3/a. Given that the precipitation decreases 1 mm, the runoff of Black and White Rivers decreased by 0.02×108 m3 and 0.05×108 m3, respectively. Correspondingly, in an increase by 1 mm evaporation, the runoff of Black and White Rivers decreased by 0.12×108 m3 and 0.27×108 m3, respectively. The annual increase of water storage in Zoige Plateau is(59.30±0.1869)×108 m3, annual average reduction rate is 0.49×108 m3/a from 1981 to 2011. This study will be helpful to understand the importance of the Zoige Plateau for water resources safety in the upper Yellow River.