By analyzing precipitation and tide level data of the Guangdong-Hong Kong-Macao Greater Bay Area (GBA) from 1960 to 2020, and combining the Thiessen polygon method with correlation analysis, the non-coincidence phenomena and spatial distribution characteristics of rainfall-tide compound disasters and storm surges were revealed. The results indicate that the non-coincidence of storm surges in the GBA is significant. Specifically, the variation points in the estuary regions are concentrated around 1987, whereas those in the upstream basins occur earlier, around 1975. For rainfall-tide compound disasters, the variation points are observed around 1987 in the estuary areas but are delayed to 1994 in the central basin. The non-coincidence of storm surges is primarily driven by climate change and human activities, such as upstream dam construction and estuarine sand mining. Furthermore, the variations in compound disasters are significantly influenced by the interaction between storm surges and rainfall.