Taking the midstream and upstream of Bortala river as the study area ,the paper used the methods which are statistical analysis,Mann-Kendall nonparametric test and analysis parameters of hydrological characteristics and the data that are monthly runoff,precipitation and temperature on Wenquan and Bole station in 1992~2012 to analyze the impact of climate change on runoff.The results showed that runoff in midstream and upstream of the Bortala river appeared a trend of increase since 1990s.Runoff increased obviously in nearly 10 years.The interannual variability of runoff at upstream was stable.The annual variability of runoff was opposite, and runoff change at upstream had characteristic of hydrothermal same period. however，that of the midstream had a lag. The temperature is the main factor which causes runoff change at the upstream.The agricultural irrigation,temperature and precipitation are the main reasons of runoff change at the midstream.The influence of temperature on runoff is the most significant.