The South China Sea (SCS) is one of the world’s most productive fishing zones. Regionalising the SCS, particularly the understudied southern sector (SSCS), is crucial for improving resource management in the SCS. In this study, we analysed 24 years of satellite-derived chlorophyll-a concentration (CHL) using a combination of empirical orthogonal function and Fuzzy C-mean clustering techniques. Our results reveal that the seasonal variability of CHL can be divided into three distinct regions. Broadly, these regions separate into the eastern and western basins. The first region encompasses the eastern boundary of the SSCS, the second region includes the area off the coast of Vietnam, and the central SSCS, while the third region extends from Karimata Straits to the Mekong River mouth. Each region exhibits unique seasonal CHL patterns: the first region shows a unimodal seasonality, while the second and third regions display bimodal seasonality. Beyond the climatological occupancy of these regions, we also demonstrate that their spatial extent is temporally dynamic. Regions can expand, contract, or shift entirely on an interannual scale. For instance, during the 1998 El Niño event, CHL variability in the deep basin experienced a marked changed due to intense warming. In contrast, during the 2015 El Niño event, despite similarly intense warming, CHL variability was statistically consistent with climatological norms. While the modulation of monsoonal winds by El Niño Southern Oscillation partially explains the interannual variability in the region. Our findings suggest that this variability is highly complex, likely due to the dynamic nature of the basin.