Based on the precipitation and runoff data from 1961 to 2017 in the eastern source area of the South-to-North Water Transfer Project, the rainfall variation character and runoff evolution law in the source area were analyzed using the cumulative anomaly method, Mann-Kendall testing method and Morlet wavelet analysis method. The results showed that the variation of rainfall in the source area was consistent with that in the Huaihe River Basin. The variation of runoff in the source area was consistent with that of rainfall, but the degree of variation was much more dramatic, reflecting the significant influence of natural factors and human activities, especially the large number of water conservancy projects in the basin. The annual rainfall was mainly concentrated in summer, and the annual rainfall and summer rainfall increased non-significantly. Annual runoff mainly concentrates in the period from July to September, and showed a non-significant decreasing trend. Since the 1980s, the uneven coefficient of interannual runoff in the source area increased, which was more than four times that of the interannual rainfall. In the future, the source area will enter a flood period of about nine years. Under extreme weather conditions, it will face a severe situation of flood control.