According to the Chinese climate divisions and the Huang-Huai-Hai River basin digital elevation map, the basin is divided into seven sub-regions by means of cluster analysis of the basin meteorological stations using the self-organizing map (SOM) neural network method. Based on the daily precipitation data of 171 stations for the years 1961–2011, the drought frequency changes with different magnitudes are analyzed and the number of consecutive days without precipitation is used to identify the drought magnitudes. The first precipitation intensity after a drought period is analyzed with the Pearson-III frequency curve, then the relationship between rainfall intensity and different drought magnitudes is observed, as are the drought frequency changes for different years. The results of the study indicated the following: (1) the occurrence frequency of different drought level shows an overall increasing trend; there is no clear interdecadal change shown, but the spatial difference is significant. The occurrence frequencies of severe and extraordinary drought are higher on the North China Plain, Hetao Plains in Ningxia-Inner Mongolia, as well as on the Inner Mongolia and the Loess Plateaus, and in the Fen-Wei Valley basin. (2) As the drought level increases, the probability of extraordinary rainstorm becomes lower, and the frequency of occurrence of spatial changes in different precipitation intensities vary. In the areas surrounding Bo Sea, the Shandong Peninsula and the Huai River downstream, as the drought level increases, the occurrence frequency of different precipitation intensities first shows a decreasing trend, which becomes an increasing trend when extraordinary drought occurs. In the middle and upper reaches of the Huai River basin, on the Hai River basin piedmont plain and Hetao Plains in Ningxia-Inner Mongolia, Inner Mongolia and Loess Plateaus, and in the Fen-Wei Valley basin, the probability of the different precipitation intensities shows an overall decreasing trend. The mountains with high attitude and Tibetan Plateau are located at high altitudes where the variation of different precipitation intensities with the increase in drought level is relatively complex. (3) As the drought frequency increases, areas I, II and V which are located on the coastal and in the river basin are vulnerable to extreme precipitation processes; areas III, IV, VI and VII are located in the inland area where heavier precipitation is not likely to occur.