Climate change has profound impacts on runoff change processes, it is the important cause of the water resources shortage and ecological environment desertification in the arid area of northwest China. Based on the monthly runoff and meteorological data at the upper reaches of the Aksu River Basin during 1961-2014, the linear regression, the Mann-Kendall non-parametric statistical test, and the Pearson correlation coefficient methods were used to analyze the runoff evolution characteristics of Aksu River Basin and its responses to climate change. The results showed that: in recent 54 years, the runoff in the Aksu River Basin had a significant upward trend, and the climate had a warmer and more humid trend. The runoff element and climate factors had good temporal consistency, and the mutation time occurred in 1990s, the abrupt change time of runoff was slightly behind the temperature and precipitation. By the statistical correlation analysis, the exit-mountain runoff was affected by both temperature and precipitation in Aksu River Basin. The runoff of the Tuoshigan River was more sensitive to temperature, while the precipitation affected the runoff more for the Kumalake River.