Base flow is the main supplement source of stream flow in dry period and especial important to the river in arid and semi-arid area. It plays an important role in maintaining the fragile ecological system in the region. Based on the observed runoff series of Hailiutu river from 1957to 2007, the paper used recursive digital filter method for base flow separation and investigated the trend of annual and inter-annual variations of base flow and BFI (base flow index). The statistical method of nonparametric Mann-Kendall test was used for analyzing the trend of base flow and BFI. Results showed that base flow holds a larger proportion of the runoff, annual base flow and runoff have a significant descending trend; the annual distribution of runoff is even but the base flow first decreased and then increased; BFI both in annual and inter-annual shows even, has no significant increase or decrease trend. The Regime Shift Index (RSI) method was used to measure sudden change point of the base flow in 1966and 1986.The runoff occurred sudden change in 1968,9and 2001.