The yearly rainy days with different rainfall level and annual precipitation were obtained by using the daily precipitation data (1960-2004) of 17 stations in the Qilian Mountain. By means of EOF and REOF analysis on normalized annual precipitation, the abnormal spatial distribution and the time evolvement of annual precipitation there were investigated. Results show that the climate average distributions of annual precipitation and different level rainy days were similarity in geographical distribution. Both the annual precipitation and the different level rainy days were evidently more in the west side than that in the east side of the same latitude area, and more in the east section than that in the west section of the Qilian Mountain, and the isoline presented the direction of northwest to southeast. The spatial anomaly of the annual precipitation characterized the coincident variability in the whole area at first, and then the adverse trends in the east and the west part. The rotated loading vectors reflected 4 anomaly modes of the north slope of the west section, the east section, the south slope of the west and middle section, and the north slope of the middle section of the Qilian Mountain. In recent 45 years, the decadal change in precipitation was obvious in the north slope of the west section and relatively small in the other three areas. Wavelet analysis shows that the precipitation period changes were different in four areas, and that means the complexity of the annual total precipitation over the Qilian Mountain.