Oceanic submesoscales can significantly influence phytoplankton production and export. Based on two-year Biogeochemical Argo (BGC-Argo) observations, this study investigated the development of submesoscale instabilities (particularly symmetric and mixed-layer baroclinic instabilities) and their impacts on biological production and export in the oligotrophic South China Sea basin. In the northern basin, winter blooms consistently cooccurred with seasonally deepened mixed layers reaching the nutricline. However, significantly stronger and weaker winter blooms were observed over two consecutive winters within the observational period. During the first winter, when the mixed layer was approximately 20–30 m shallower than the nutricline, symmetric-instability-induced upward nutrient entrainment played a crucial role in initiating strong synoptic blooms in early winter, which were approximately 20–30 days earlier than the contact between the seasonally deepened mixed layer and mesoscale-cyclone-induced uplifted nutricline. Meanwhile, symmetric instability also facilitated the export of fixed phytoplankton carbon from the surface to deeper layers. Conversely, during the second winter, remarkably intense mixed-layer baroclinic instability associated with an intense mesoscale anticyclone led to more significant shoaling of the mixed layer compared to the nutricline, thus increasing the vertical distance between the two layers. As a result, upward nutrient injection, phytoplankton bloom, and carbon export were suppressed. Compared to the northern basin, the significantly shallower mixed layer in the central basin revealed significantly inhibited phytoplankton biomass and submesoscale instabilities during winter. Future work will integrate high-resolution numerical models to further reveal the modulations of submesoscales on the spatiotemporal variability of primary production and export in South China Sea.