The biological pump sequesters atmospheric CO₂ into the deep sea for long periods of time through the deposition of particulate organic carbon (POC). However, the composition and regulatory mechanisms of POC flux vary considerably across different ecosystems. In this study, we explored the compositional differences in POC export flux and the potential influencing factors of three different ecosystems, the shelf, the slope and the basin. Our data set consisted of six summer cruises at four stations in the northern South China Sea during 2014-2018. Based on the flux assessment of sediment traps, we revealed a gradual decrease in POC flux from the euphotic zone as moved away from the continental shelf. The integrated average POC flux in the euphotic zone of the shelf was 2.5 times higher than that of the slope and 4 times higher than in the basin. Additionally, the type of the main settling POC flux was observed to change from aggregates to zooplankton fecal pellets. The stark differences in sedimentation flux across ecosystems are closely tied to phytoplankton biomass and community structure: higher biomass correlates with higher POC flux. Additionally, ecosystems with a higher proportion of diatoms exported greater POC flux. In cases of lower biomass, community structure becomes an even more critical factor in regulating POC flux. Moreover, through the use of a regionalized ocean model combined with in-situ and remote sensing data, we suggest that physical processes such as eddies and internal waves influence the vertical distribution of POC flux in the euphotic zone, potentially enhancing the carbon storage capacity of certain areas. Further analysis of the distribution characteristics and regulation of POC export flux in marginal seas such as the South China Sea, where the environmental gradient is highly variable, will contribute to more accurate assessments of the biological pump's carbon storage potential in these regions.