[Objective] The aim was to study climate changes in northern Tianshan in Xinjiang and its influences on runoff. [Method] Based on the runoff data for 54 years of Kenswatt station on Manas River and the climate date of 16 meteorological stations from 1957 to 2007 in the north of Tianshan in Xinjiang, the climate change and temporal series of the annual runoff were studied by use of nonparametric test, wavelet analysis, R/S analysis and periodic trend superposition model. [Result] The temperature, precipitation and annual runoff of Manas River increased significantly. The Hurst coefficients of both climate factors and the annual runoff were bigger than 0.5, which indicated that they would still keep an increasing trend. Temperature from 1957 to 1959 was low, precipitation was much, belonging to low temperature and more rain period. 1960s and 1970s were low temperature and less rain period. Temperature in 1980s was close to average value and precipitation was little. Since 1990s, it entered into high temperature and less rain period and was significant during 2000 and 2007. The temperature and precipitation changed in 1995 and 1996. Temperature was significant in 11 and 22 years. Precipitation had 5, 8, 14 and 22 years of main cycle. The annual runoff and climate factors in Manasi River were increasing in different times. The annual runoff was related to climate factors, and temperature was closer to annual runoff than precipitation. [Conclusion] The study provided theoretical basis for the reasonable configuration, ecological protection and agricultural production of water resources in north Tianshan in Xinjiang.