Abstract Hydrologic drought, considered as a typical natural phenomenon in the background of global climate changes, is the continuation and development of meteorological and agricultural droughts, and is the ultimate and most thoroughly drought. The research area controlled by the 55 hydrological sections in South China is selected in this paper, and the intensity and frequency of hydrologic droughts are analyzed by the Standardized Runoff Index (SRI), and the driven mechanism of watershed lithologies to hydrologic droughts is discussed. The results show that (i) the hydrological drought of Karst drainage basins is shown the gradual aggravation from the west to east parts in South China, with the significant north–south stripe distributions at the SRI_3 and SRI_6; (ii) the occurring probability of hydrological droughts is the Limestone-type Karst Basin (II and III, 0.17) < Dolomite-type Karst Basin (I and IV, 0.22) < Non-Karst Basin (V, 0.25) in terms of combination types of basin lithologies, and (iii) the Karst Basin (I and III, 0.18) < Semi-Karst Basin (II and IV, 0.2) < Non-Karst Basin (V, 0.25) in terms of basin lithologies. Therefore, this proves that the most water-stored spaces are found in Karst Basins under the differential dissolution or erosion effects of soluble water, followed by in the Semi-Karst Basin, the least water-stored spaces in the Non-Karst Basin.