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Abstract Mesoscale and submesoscale processes have crucial impacts on ocean biogeochemistry, importantly enhancing the primary production in nutrient‐deficient ocean regions. Yet, the intricate biophysical interplay still holds mysteries. Using targeted high‐resolution in situ observations in the South China Sea, we reveal that isopycnal submesoscale stirring serves as the primary driver of vertical nutrient transport to sustain the dome‐shaped subsurface chlorophyll maximum (SCM) within a long‐lived cyclonic mesoscale eddy. Density surface doming at the eddy core increased light exposure for phytoplankton production, while along‐isopycnal submesoscale stirring disrupted the mesoscale coherence and drove significant vertical exchange of tracers. These physical processes play a crucial role in maintaining the elevated phytoplankton biomass in the eddy core. Our findings shed light on the universal mechanism of how mesoscale and submesoscale coupling enhances primary production in ocean cyclonic eddies, highlighting the pivotal role of submesoscale stirring in structuring marine ecosystems.