As an important component of runoff, base flow is the most important headwaters in dry season in arid and semi-arid regions. The process of base flow is closely related to climate and cryosphere changes. This article focuses on Shule river basin, Heihe river basin and Shiyanghe river basin in Qilian mountains of the Hexi island. Based on daily runoff data, the recursive digital filter is used for base flow separation. Before using this method to separate base flow, the parameter and number of filtering should be calibrated. Through the comparison, determine the filter parameter and calculated the base flow, and on this basis, analyzed the changes of base flow, and then the affecting factor on the changes of base flow from two aspects of climate change and cryosphere changes is discussed. Through the above research, following is the main conclusions:（1）The spatial variation of base flow value in Hexi island is gradually reduce from midland to west and from west to east. （2）The base flow inter-annual fluctuation of western and central regions are severe and overall shows increasing trend. The decadal variability of base flow index shows that at decadal scale, the proportion that base flow accounts for the runoff is relatively stable.（3）In general, the base flow value in summer and autumn at the western and central region of Hexi island have increasing trend and reduced in eastern. Base flow values are relatively stable in winter and spring.（4）Inter-annual variation trend and wave process of base flow is similar with precipitation. Analyzing the relationship between base flow variation and runoff in summer shows that there is significantly correlation between the two
Precipitation is a major influence factor to the change of base flow in Hexi island and temperature is an indirect factor. Rising temperatures will lead to the increase of ice and snow melt and permafrost degradation. The increasing of glacial meltwater is good to base flow recharge. The degradation of permafrost increases activity layer thickness, slow down the recession process of runoff in winter and increases the supply from underground runoff to river.