To better address water scarcity and water security issues in Central Asia,careful and prudent water resources allocation planning and management requires detailed and reliable knowledge of hydrological changes. Based on the runoff and meteorological records from Khorugh during the period of 1940 - 2017,the runoff variations of the Gunt River and its response to the climate change was analyzed using the non-uniform coefficient,linear trend method,Mann-Kendall test,R/S and wavelet analysis in this paper. The main results were obtained as follow: (1) the seasonal distribution of runoff was quite uneven,and 75% of runoff was occurred at June- September (around 19th July), and the peak periods showed no significant advance or delay. (2) Annual runoff series showed a decreasing trend which was not remarkable. High runoff occurred during 1940 - 1959 and 1977 - 1995. Low runoff occurred during 1960 - 1976 and 1996 - 2017. According to the results of R/S analysis,annual runoff will increase in the future. Wavelet analysis showed that the remarkable 23 - 34 year,9 - 22 year and 4 - 8 year periodicities were found in annual runoff series. (3) The intra-annual precipitation had some significant effects on the runoff variations of the Gunt River,and the average temperature was synchronous with the seasonal variation of discharge. The annual runoff variation was controlled by precipitation. The cross wavelet showed that 2 - 5 year cycles were occurred in the whole time domain,and 8 - 12 year cycle was found during the period 1960 - 1980.