The oligotrophic ocean, mostly located in subtropical regions occupies ~40% of the Earth surface and has been conventionally regarded as an ocean desert. It is characterized by permanent stratification, nutrient depletion and extremely low net biological production, and hence, contributes little to carbon export from surface to deep waters at per unit area. Emerging evidence has shown that this oceanic system has a much larger dynamic range of nutrient inputs from different sources in addition to those from depth. These differently sourced nutrients with differing stoichiometry may stimulate biological productions in different community structures and drive the carbon export at various depth horizons within the sunlit euphotic zone (EZ). Hence, the EZ is better characterized by a two-layered structure with a nutrient-depleted layer (NDL) above the nutricline and a nutrient replete layer (NRL) across the nutricline to the base of the EZ. Based on simultaneous turbulence microstructure and high-resolution chemical measurements, we quantified diapycnal fluxes of nitrogen, phosphorus, silicon, and carbon in the oligotrophic South China Sea showing a negligibly low diapycnal dissolved inorganic nitrogen (DIN) flux in the NDL where other nutrient supplies sustain the new production. Here, higher phosphate and silicate fluxes relative to DIN than Redfield stoichiometry further indicate N-limited biological productivity and additional removal of DIN by diatoms. In the NRL, the DIN flux is sufficiently large in supporting the export production therein. Here, higher dissolved inorganic carbon (DIC) flux relative to DIN than Redfield stoichiometry further infers DIC excess in the upper ocean of oligotrophic nature. Considering the new understanding of the biogeochemistry of the oligotrophic ocean, we attempt to propose an improved framework of nutrient-determined and biologically mediated carbon export in the ocean desert.