Based on the SWAT(soil and water assessment tool, SWAT) model and Mann-Kendall method, the spatio-temporal change of blue water and green water resources in different growing season over the source of the Yellow River from 1961-2010 were analyzed. The results showed that the amount of green water resources was generally 2 times of blue water resources in the source region of the Yellow River. Blue water resources in spring and autumn showed a declining trend, and significantly decreased by 0.355 mm/a in autumn, while a weak increasing trend in summer. Green water resources showed an increasing trend in summer and autumn, and significantly increased by 0.286 mm/a in autumn, while decreasing trend in spring. From southeast to northwest, blue water and green water showed progressively decreasing trend. In the southeast, blue water resources decreased by 1.98 mm/a in autumn while green water resources increased in summer and autumn with the largest slope 1.62 mm/a. Because of global climate changes, the spatiotemporal difference in blue water and green water resources will be further increase. Hence, it is urgent to strengthen the systematic management of water resources in the source region. And the amount of inefficient water consumption and the high water consumption crops should be reduced. Thus the supply of water in the lower and middle reaches of the Yellow River can be guaranteed.