In summer, the Madden-Julian Oscillation (MJO) greatly influences the intraseasonal variability of the South China Sea (SCS). Previous studies have revealed MJO effects on surface chlorophyll (Chl) concentration, but the impact of the MJO on the ecosystem's structure and functionality remains unexplored. Here, we investigated the marine ecosystem response to the MJO by analyzing phytoplankton pigment data collected in cruises from 2010 to 2014. The results indicated the strong influence of the MJO on the structure of phytoplankton size classes (PSCs) in the upper 50 m of the SCS basin. To further explore the ecosystem's response to MJO, we utilized a well-calibrated physical-biogeochemical model (ROMS-CoSiNE) of the SCS to conduct numerical experiments with and without MJO forcings. Our model demonstrated that MJO-induced deep mixing and upwelling increased nutrients in the upper layer, increasing the Chl concentration with a higher proportion of nanophytoplankton (15 %) and a lower proportion of picophytoplankton (−20 %). Moreover, The MJO-forced model experiment exhibited a substantial enhancement in primary production (56 %) and export production (23 %), resulting in a notable decrease in the e-ratio. This reduction in the e-ratio cannot be attributed to changes in PSCs but can be explained by the time lag between primary and export production. This lag was prolonged by the physical processes of upwelling and mixing, which slows down the particle sinking. Our results emphasize the important role of MJO in regulating the ecosystem at intraseasonal scale, thus improving our comprehension of the nonsteady dynamics of ecosystems in the SCS.