As the biggest reservoir in the North China, the Miyun Reservoir is an important water source to ensure water supply security and economic and social development in Beijing. The Zhangjiafen station and Xiahui station were chosen as representation stations. Based on the annual runoff from 1960 to 2008, the change trend of the runoff in the upstream of the Miyun Reservoir was analyzed by using linear regression method, Kendall rank correlated test method and Spearman rank correlated test method. The period of the runoff in the upstream of the Miyun Reservoir was studied by using continuous power spectrum method. The results indicate that the annual runoff variations of the Chaohe River and Baihe River are both large, and they have almost the same abundant and low state in the same year. Among them, the probability of simultaneous appearance of abundant or low state is the biggest. During the past half century, the runoff of two watersheds showed an obvious decrease trend, and the Baihe watershed decreased faster than Chaohe. Meanwhile, there is an obvious 4-5 years oscillation period of annual runoff series in the upstream of the Miyun Reservoir.