Using the EOF and REOF methods and rainfall data of 42 weather stations in Qilian mountain and its surroundings, the spatial variation of annual rainfall in Qilian mountains is summarily analysed and divided three subregions.By combining grid analysis method, GIS technology, as well as aiming at rainfall distribution in the middle and east of Qilian mountains, the fitting study of annual rainfall is done and the complex variation of simulated rainfall in space is analyzed.The results show that the local rainfall distribution can be obtained by applying those methods, local rainfall and the observed rainfall at station are identical, at the same time, the terrain of Qilian mountain area can be reflected by local rainfall of grids, and its rainfall distribution provides the scientific basis for the water source distribution in Heihe valley.