Based on the observed monthly runoff data for 52years(1957-2008) in 5hydrological stations in headstream areas and the Alar station in the mainstream areas, the paper studied the runoff periodicity, abrupt change and the coming period trends by using the methods as time series periodic variance analysis extrapolation, nonparametric test, and R/S analysis. The results showed that the jump points of the two streams in Aksu river happened in 1993and its runoff held significant increasing trend and will last for a long time in the coming period. The annual runoff tendency of Tongguzlok and Uruwat was just the reverse without abrupt change. the Yarkant River expressed a slightly increasing trend and its jump point was in 1993, which will turn to decrease trend; Theses aspects, for example abrupt change, annual runoff trend, total annual runoff volume and so on, are not consistent in headstream and mainstream of the areas, which dictates that the annual runoff process is significantly affected by human activity.