The regional climate model (RegCM3) is used to simulate the summer (June to August) climate from 2000 to 2006 over the Kaidu River Valley. The results reveal that the model has a good ability to reproduce the distribution of precipitation and temperature. The altitude, observed data and simulated data are used to revise the simulated temperature and precipitation, and then the areal rainfall and average temperature are calculated. It is proved that there is a good consistency between runoff and precipitation over the Kaidu River Basin, and R2 is 0.97. The analyses of the summer average temperature, areal rainfall and runoff show that the main impact factor of Kaidu River’s runoff is precipitation. The reason why temperature makes a negative contribution to runoff is probably because of the reducing of the small and middle sized glaciers, which causes the runoff to decrease and temperature to rise. The other reason maybe is the rise of temperature, which can lead to the increase of evapotranspiration.