Based on topographic maps, remote sensing images, meteorological and hydrological data, glacier change and its impact on water resources are investigated in the Kuytun River Basin under the background of climatic change. Results show that glacier area decreased by 65.4 km~2 with a retreating rate of -32.6%, 31 glaciers disappeared, and mean glacier area reduced by 0.19 km~2 from 1964 to 2015. Loss of glacier volume is approximately 4.39 km~3 with an annual loss rate of 0.084 km~3 in 52 years. APAC(Annual percentage of area change)increases since 2000,which indicates that accelerated glacier shrinkage is observed. Annual mean temperature in the basin exhibits a marked rising trend over the study period with a tendency rate of 0.39℃/10a. Results of MK(Mann-Kendall) mutation test indicate that mutation point of annual mean temperature occurs in 1988, and annual mean temperature increased rapidly since 1988.There is no mutation year for annual precipitation, which exhibits a slightly decreased tendency from 1964 to 2009. Present- day glacier shrinkage is a mix response to past and current climate fluctuation, and glacier ablation is highly correlated to the positive accumulated temperature over the ablation period, while accumulation is originated from the annual precipitation. The analysis shows that expenditure of glacier mass (ablation) caused by the positive accumulated temperature increase during the ablation period larger than mass income (accumulation) originated from annual precipitation is the main reason for glacier retreat. There is a rising trend for annual runoff with a tendency rate of 0.13*10~8m~3/10a from 1964 to 2010, and mean annual runoff is approximately 6.54*10~8m~3. Annual runoff is on the decline from 1964 to 1993, but displays an upward tendency since 1993. Results of wavelet analysis show that there exists the periodic fluctuation of 3-15 years approximately for annual runoff, which also change since 1993, and maximum wet season appears in the period of 1995-2000. Results of MK mutation test show that no mutation year is found for annual runoff in 47 years. Net loss of water resources caused by glacier ablation is approximately 39.5*10~8m~3 with an annual loss rate of 0.76*10~8m~3/a, which accounts for 12% of mean annual runoff over the study period. Affected by climatic warming, glacial meltwater increased since 1980s and its proportion in annual runoff rose. Besides, glacier coverage of the basin decreased by 3.4% in 52 years. With the ice loss gradually, the contribution of glacial meltwater to runoff would decrease step by step in the future forecasting warming scenario. Despite the importance of glacier for the local hydrological cycle, there is urgent necessity to reinforce the monitoring and study of glacier status, which could provide the better decision-making value for assessment, allocation and sustainable utilization of local water resources.