Abstract: The empirical orthogonal function (EOF) is a commonly analytical tool in climate study. But because of the constraints of the method itself, not all the leading EOF modes can reveal the true climate mode from the climatological data in some cases. Based on the daily precipitation datasets from the basic stations over the Huaihe River Basin from 1961 to 2009, the climatological statistical characteristics of the rainstorms in the Huaihe River Basin are studied by using the Distinct EOF (DEOF) method. The results show that DEOF-1 displays contrary changes in the south-north direction on the rainstorm precipitation in the Huaihe River Basin, which means that when the rainstorm precipitation of the central and southern region is more (less) than normal state, the northern region is less (more) than normal state. The first principal component has obvious periodic oscillations of 16-17 years, suggesting that the drought and flood in southern and northern region show a decadal oscillation; DEOF-2 displays the abnormal changes of the rainstorms in the central region of the Huaihe River Basin, and the second principal component has a obvious linear trend showing a upward trend in the last 50 years and a convertion from less to more than normal at about 1990. Comparing with the EOF analysis, DEOF can effectively exclude the spatial characteristics related hiqhly to the stochastic diffusion model, catch the features having significant differences with the model and display the features more prominently, and detect physical signals from a strong background noise, and therefore it should be a better estimate for the true climatic mode.