The export of phytoplankton-synthesized particulate organic carbon from the upper ocean to the depth removes CO₂ from the atmosphere, playing a critical role in the global climate system. The South China Sea (SCS) is the largest marginal sea in the western Pacific. However, current understanding of carbon export in the SCS, particularly its interannual variability, remains limited due to sparse observations and large discrepancies among different estimation methods. This study firstly reconstructed a high-accuracy nutrient dataset, upon which we developed a one-dimensional ecosystem dynamics model. The model successfully reproduced nearly three decades (1993–2021) of interannual variations in nutrients, chlorophyll, phytoplankton, zooplankton, and detritus at SEATS. Based on the model outputs, we quantified export production at SEATS. Results show that export production at 100 m depth ranges from 0.06 to 22.44 mmol C m⁻² d⁻¹, with an average of 3.58 mmol C m⁻² d⁻¹. Seasonally, export production is lowest in winter (December–February), at ~0.55–2.27 mmol C m⁻² d⁻¹, rises rapidly in spring (March–May) and peaks in April at 9.50 mmol C m⁻² d⁻¹, then gradually declines during summer–autumn (June–November) from 7.54 to 0.96 mmol C m⁻² d⁻¹. Interannually, export production was lowest in 1999 and highest in 2005, with an overall significant declining trend over the study period. Correlation analysis indicates that particulate organic carbon (POC) export flux is positively correlated with surface nitrate concentration (R²= 0.17) and strongly negatively correlated with nutricline depth (R²= 0.73), suggesting that nutricline variability is the primary regulator of interannual POC export. In addition, shortwave radiation shows a weak positive relationship (R²= 0.09), indicating a minor role of light. Further analysis reveals a positive correlation with Kuroshio intrusion (R²= 0.14) and a negative correlation with sea surface height anomaly (SSHA, R²= 0.20), implying a dominant influence of large-scale upwelling on carbon export. In contrast, the effects of mixed layer depth, vertical velocity, and wind speed are weak (R²< 0.05). Overall, this study highlights the interannual variability of export production in the SCS basin and provides a scientific basis for understanding long-term changes in the SCS carbon sink and its future projections.