Accurate estimation of particulate organic carbon (POC) export efficiency in the euphotic layer is essential to understand the efficiency of the ocean’s biological carbon pump, but field measurements are difficult to conduct and data are sparse. In this study, we investigated the relationship between POC sinking export efficiency and ocean net primary production (NPP) in the euphotic layer of the northern South China Sea (NSCS), with the help of high spatiotemporal coverage satellite-derived NPP. Annual mean POC export efficiency in euphotic zone is 34% for the shelf areas and 24% for the basin of the NSCS in the context of satellite-derived 16-day-composited NPP. Similar to what is generally observed in the global ocean, the POC export efficiency on the shelf areas appears to be strengthened with the increase of NPP. However, in the basin areas, the opposite relationship is observed. That is, the POC export efficiency significantly decreases with the increase of NPP. Seasonal decoupling between NPP and POC export, phytoplankton size structure, grazing by zooplankton, and dissolved organic carbon export might account for the observed negative relationship between the POC export efficiency and NPP in the euphotic layer of basin region. System comparison between shelf and basin would be helpful to promote understanding of the regulation mechanism of POC export in the tropical marginal seas.