Due to an absence of an essential daily data set, changing characteristics, and cause of flow extremes in the Tianshan Mountains are rarely explored in depth. In this study, daily based long-term meteorological and hydrological observation data were collected in four typical watersheds in the middle Tianshan Mountains; Manne-Kendall trend analysis and Pettit’s test were used to detect the trends and alterations of extreme flow series; Generalized Extreme Value distribution (GEV) and General Pareto distribution (GDP) models were used to describe the probability distributions of annual maximum (AM) and peaks over threshold (POT) series based on daily discharge; and the relationship between extreme flow and climate indices, were also investigated. The findings indicated that, change of the AM series at five hydrological stations experienced positive trends; the POT series generally showed no significant trends, while the peaks over threshold number (POTN) present a positive trend at the five stations. Change points exist in the POT and occurrence time of maximum daily discharge in spring (AM-SPR) series at the Kensiwate (KSWT) station in Manas watershed; the mean extreme flow decreased after 1986, and the occurrence time the annual maximum daily flow in spring significant forward after 1978. The AM series can well fit the GEV distribution, while the POT series fit the GDP distribution better; the GEV model performed worse in estimating flood events with high return period than low return period events. Moreover, acceleration of glacier melting lead to the magnitude and frequency increments of flood in the north slope; intensifying and frequent precipitation extremes are dominate factors of extreme flow variations in south slope watersheds which without large amount of glacier coverage; and continually temperature rising in spring and increased precipitation in winter lead to the change on magnitude and timing of spring extreme floods.