In order to provide a scientific basis for the planning and operation of the South-to-North Water Transfer Project, the characteristics of precipitation and runoff changes in the project area since 2001 are identified based on more complete hydrological observation data than those in the level years formulated in “General Plan of the South to North Water Transfer Project”. Mann-Kendall trend test, wavelet analysis and other methods are used to analyze the statistical difference and variation characteristics of precipitation and runoff between the comparison period (2001—2016) and the reference period (1956—2000). The results show that compared with the reference period, the precipitation in the water diversion area has no obvious change in the comparison period. The natural runoff of Datong Hydrologic Station on the Yangtze River decreases by 3.5%, and the water resource conditions in the water diversion area are relatively stable. The precipitation in the water receiving area in the comparison period is basically unchanged compared with the reference period, and the natural runoff is 3.9% higher. However, the natural runoff in the water receiving area of Shandong Province, Hebei Province and Tianjin City decrease by 6.6%, and the natural runoff in the three provinces and city show a significant decline trend.