Holoplanktonic molluscs, though often overlooked, are ecologically vital zooplankton that significantly contribute to marine food webs and the carbon cycle, yet their population surges under environmental change can trigger ecological disasters. To elucidate the environmental drivers of their community structure, we investigated the diversity and abundance of these organisms in the northwestern South China Sea (NWSCS), identifying 39 species—24 pteropods and 15 heteropods—with pronounced seasonal and regional variations. Species richness was higher in offshore than nearshore waters during both summer and winter, while abundance peaked sharply in summer, particularly in areas influenced by cyclonic eddies and coastal upwelling. Statistical analyses revealed that temperature, salinity, and chlorophyll a were key factors shaping assemblage composition, with Creseis acicula serving as a robust indicator for nearshore waters across seasons, whereas Limacina bulimoides and Heliconoides inflatus emerged as the best indicators for offshore summer and winter, respectively. These results establish a critical baseline for understanding holoplanktonic mollusc distributions in this northwestern Pacific marginal sea and offer a solid scientific foundation for zooplankton monitoring and sustainable ecosystem management in a rapidly changing ocean.