Abstract: Mesoscale eddies and embedded submesoscale dynamics critically dictate ocean biogeochemistry; yet, how their fine-scale physical–biological coupling modulates phytoplankton community assembly and diazotrophic activity across eddy life stages remains elusive due to observational limitations. Here, using a targeted high-resolution (~10 km) multi-parameter survey in the northern South China Sea, we unravel the fine-structure of eddy-driven physical–biological interactions across distinct developmental stages of cyclonic and anticyclonic eddies. Submesoscale features—including fronts, strain, and secondary circulations—generate pronounced nutrient patchiness, which interacts with top-down grazing pressure (resolved via copepod gut metabarcoding) to restructure phytoplankton communities. Ochrophyta dominates resilient, diverse eddy margins, whereas decaying cyclonic cores are dominated by Gyrodinium with depleted diversity and dispersal limitation. Conversely, intensifying anticyclonic eddies select for the mixotrophic picophytoplankton Chloroparvula pacifica (24.0 ± 4.5%). Crucially, submesoscale frontal dynamics, intrinsically linked to intense turbulent dissipation, drive advective transport and convergence to aggregate nutrients and Trichodesmium spp., creating biogeochemical hotspots where N₂ fixation sustains 20%–30% of primary production nitrogen demand. Our findings demonstrate that stage-specific submesoscale physics strictly govern upper-ocean community succession and nitrogen resupply, highlighting the imperative of integrating submesoscale turbulent processes into global ocean ecosystem models.