In order to analyze the spatial structure and multi-scale characteristics of runoff time series in the Yarlung Tsangpo Zanggo River basin, the monthly runoff data at 6 meteorological stations in the study area from 1956 to 2000 are investigated. The periodic oscillation of runoff variation and the points of abrupt change at different time scales are investigated by using wavelet method in this study. At the same time, the main periods of each time series are identified by estimating wavelet variance, which is helpful to determine the spatial distributions of periodicity. Application of the Morlet wavelet function for the runoff time series has shown that the seasonal and annual trends of runoff change in the last 44 years were consistent at the scale of 15 years, and the abrupt change occurred mostly in 1957, 1967, 1976, 1983 and 1992. There are more points of abrupt and more numbers of alternation between low flow and ample flow at the smaller scales. There is an obvious periodic oscillation of 15 and 2 years for the first main periods for the seasonal and annual runoff variation, and 15, 6 and 2~3 years for the second main periods. The spatial distributions of periodicity for autumn and annual runoff time series are similar to some degree with those of winter and summer runoff, respectively. Both seasonal and annual runoff at any scales in the Yarlung Zangbo River basin will increase in the near future except the spring runoff in the Lhasa River basin at the scale of 2~3 years. The characteristics of runoff time series such as long-term trends, points of abrupt and periodic oscillation are consistent well with those of precipitation time series in the study area. It has been shown that the runoff recharge is mainly from precipitation in the Yarlung Zangbo River basin.