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This paper studies the variation of runoff of Red River Basin and discusses the influence of “corridor-barrier” functions of valleys and mountains on variation of runoff by using GIS and statistic methods based on the monthly precipitation, temperature and evaporation data from 1960 to 2000 at 32 meteorological stations in Red River Basin, and the annual runoff data of Yuanjiang River, Lixian River and Panlong River from 1956 to 2000. The results show out: (1) Under the effect of “corridor-barrier” functions of valleys and mountains in Red River Basin, the patterns of annual precipitation and runoff depth distribution in spatial change a NW-SE direction, which is similar with the trend of the Red River valley and Ailao mountains. (2) In the long temporal scale averaged over years, the most obvious effects of the “corridor-barrier” functions is on runoff variation, and the second is on the precipitation, but not obvious on the temperature. (3) Under the superposed effect of climate changes and the “corridor-barrier” functions of valleys and mountains in Red River Basin, the difference of runoff variation is obvious in the east-west direction: the runoff variation of Yuanjiang River along the Red River Fault present an ascending trend, but the Lixian River on the west side of the Fault and the Panlong River on the east present a descending trend; the annual runoff in Yuanjiang River and Panlong River had a quasi-5a periods, and Panlong River had a quasi-8a periods; the runoff variation are quite inconsistent in different periods among the three river basins.