This study utilized single-channel seismic, multi-channel seismic, and multibeam bathymetric data to examine the distribution and geomorphological background of geological hazards in the Zhongsha Islands region of the South China Sea. We elucidate the regional geological structure and its evolution while focusing on the types and characteristics of submarine hazards since the Quaternary Period. By integrating geomorphological, tectonic, and sedimentary factors, we analyzed the primary drivers of shallow geological hazards in the region. Our findings reveal that seabed topography, tectonic activity, and sedimentary processes critically influence hazard formation, particularly in geomorphic units prone to disasters, such as submarine slopes and canyons. Igneous rocks in the region display medium-acid to medium-basic compositions, with notable developmental stages during the Himalayan and Yanshan periods. From the Paleogene to the Middle Miocene, tectonic activity intensified, significantly thinning the lithosphere. By the Middle Miocene, the crust stabilized into its present configuration, marking the formation of key tectonic units in the region. Multiple phases of sedimentary evolution, influenced by the Cenozoic tectonic movements, further contribute to the region’s susceptibility to geological hazards.