The paper selects typical stations, calculates the average regional precipitation, establishes a calculation formula of natural annual runoff and calculates and analyzes the effect of precipitation variation to the runoff by utilizing the precipitation data of the region above Lanzhou, upper stream of the Yellow River and based on the basic features of temporal and spatial distribution of precipitation in the last 50 years and the relationship between precipitation of each station and natural annual runoff volume of Lanzhou Station. The results shown that the effect of precipitation variations in 1970s and 1980s to the natural annual runoff volume is not clear, while it becomes greatly notable since 1990s and the effected range reaches to 10%~20%.