As an important component of runoff, base flow is one of the most important hydrological characteristics in dry season in arid and semi-arid regions. Base flow has significant in maintaining runoff and preserving ecological environment of rivers and lakes. Based on daily runoff data from 1954 to 2009 in the upper reaches of the Shule River, the recursive digital filter and smoothed minimum method were used for base flow separation. The features of variation in base flow and base flow index, as well as the main controlling factors (temperature and precipitation), were investigated. It is found that there is a difference between the calculation results from the two methods, but the smoothed minimum method is more suitable for the study area. The average annual base flow is 6.07*10~8 m~3.As a whole, the base flow is increasing in the upper reaches of the river, similar to runoff, especially in the period of early 21st century. The base flow index is 0.66 in the study area, which is relatively stable, but whose fluctuating range is great throughout the year. In a long term, precipitation is a major influence factor to the change in base flow and base flow index. Under the background of global warming, rising temperature leads to increase snow melt and permafrost degradation, which will be increasing the supply to base flow.