Based on the three-dimensional clustering algorithm, historical hydrological drought events in the water network area of the South to North Water Diversion Middle Route Project from 1961 to 2018 were identified. The spatiotemporal evolution process of historical drought clusters and severe drought events was quantitatively analyzed, revealing the spatiotemporal encounter patterns of water deficit in the water source and water receiving areas. The potential causes of spatial differentiation of drought and the influence of water network density on drought duration were explored. The results indicate that from 1961 to 2018, multiple prolonged and large-scale extreme and severe drought events occurred in the water network area, which are basically consistent with the actual drought situation. The drought in the water source and water receiving areas shows significant spatiotemporal differentiation characteristics, which are related to differences in precipitation and underlying surface conditions. The frequency and intensity of drought in the water receiving area are significantly higher than those in the water source area. But in the 1990s, the frequency of drought in the water source area increased, and after the 21st Century, it showed a spatiotemporal asynchronous phenomenon with the water receiving area. The density of water networks has a certain regulatory effect on drought duration, but there is a marginal effect.