Based on the hydrological and meteorological data recorded for the northern and southern headstreams of the Tarim River over the last 50 years, this paper analyses the variation characteristics of high-flow and low-flow indexes of annual runoff, air temperature and precipitation using a non-parametric test. Additionally, this paper also studies the correlations between these three time series on multiple time scales for both northern and southern headstreams employing wavelet analysis. The results show the following: (i) the annual runoff and air temperature had significant increasing trends, whereas precipitation had a non-significant increasing trend for the northern and southern headstreams. (ii) Abrupt changes appeared in precipitation in the north and south in 1990 and 1986, as well as in high-flow and low-flow indexes of annual runoff in 1993 and in air temperature in 1996. (iii) In the case of the northern headstreams, there was significant periodicity of 6 years in both high-flow and low-flow indexes and air temperature and of 3 and 8 years in precipitation. In the case of the southern headstreams, there was significant periodicity of 3 and 9 years in high-flow and low-flow indexes, 5 years in air temperature, and 5 and 8 years in precipitation. (iv) The high-flow and low-flow indexes in the headstreams of the Tarim River are closely related to the air temperature and precipitation. Copyright © 2012 John Wiley & Sons, Ltd.