Clay minerals preserved in marine sediments carry important information about sediment transport processes from sources to sinks. To reveal the dynamic transport processes of clay minerals and related controlling factors in the southern South China Sea, spatiotemporal variations of clay mineral assemblages from previous studies (Cores MD05-2893, CG2, SO18287-3, MD01-2393, SO18383-3, and MD97-2150) are integrated to assess their controlling factors over the past 30 ka. Based on the smectite/(illite + chlorite) ratio in six cores, we found that the clay mineral variations on the continental slope off Sunda Shelf (Cores MD05-2893, CG2, and SO18287-3) have been controlled by the sea-level changes during the last glacial sea-level lowstand and by the East Asian monsoon during the Holocene sea-level highstand periods. Meanwhile, the clay mineral variations on the continental slope off the Mekong River (Cores MD01-2393, SO18383-3, and MD97-2150) have been driven by the chemical weathering in the Mekong River basin that associates with the East Asian summer monsoon evolution. Accordingly, we conclude that the glacial-interglacial variation of clay minerals in an integrated picture of the southern South China Sea region since the Last Glacial Maximum has been mainly controlled by sea-level change and East Asian monsoon evolution. However, these controlling factors play independent roles in different parts of the southern South China Sea, which appears more heterogeneous than generally expected.