The Heihe Basin is located in the intersection region of the Asian monsoon and westerly winds, and sensitive to climate change and ecologically fragile.Studying the response of water cycle to climate change is of great significance for understanding the current change of environment and utilization of water resources in the future.The panel data analysis method has been widely used in econometrics,but rarely used in the field of natural sciences.Based on the meteorological hydrological data from the 3 meteorological stations and hydrological stations in the upper reaches of Heihe Basin during 1959-2009, this paper applied the panel data method to analyze the influences of climatic factors on the runoff.The result of unit root test,cointegration test and granger causality test show panel data analysis method is also applicable to natural science researches.The model suggests that precipitation had a greatest contribution to runoff,and obviously,compared to the temperature,the potential evapotranspiration had a more significant effect on runoff.Results from scenario analysis showed that,with rising temperature,if precipitation increased,the driving effect of precipitation on runoff would slow down,and if precipitation decreased,the driving effect of precipitation on runoff would build up.