<p>Oceanic eddies are physical processes significantly influencing marine primary production and biogeochemical cycling. However, the impacts of the mesoscale and sub-mesoscale processes on phytoplankton communities at different development stages remain poorly understood, partly because of the observational barrier. Based on high-resolution sampling within a couple of cyclonic and anticyclonic eddies in the northwestern South China Sea, phytoplankton community structures and physicochemical parameters were studied. Our results revealed that Ochrophyta dominated at the edges of all eddies contributing to high community stability and diversity influenced by sub-mesoscale processes. However, the dinoflagellate genus <i>Gyrodinium</i> prevailed at the center of the decaying-phase cyclonic eddy, associated with the lowest diversity and stability. Chlorophyta exhibited high relative abundances in the intensified phase of anticyclonic eddy, with the mixotrophic picoplankton <i>Chloroparvula pacifica</i> (24.0 ± 4.5%) being the dominant species. Regarding community construction, the ecological niche overlap index was the highest in the cyclonic eddy center, indicting intense interspecific competition, while it was the lowest value in the anticyclonic eddy center, likely due to ecological differentiation. The neutral community model revealed that the dispersal rate of species was lower in the cyclonic eddy during the decaying phase than that during the developing phase of the anticyclonic eddy. These findings illustrate a non-uniform patchy distribution of physicochemical parameters and phytoplankton within eddy fields, emphasizing the significant role of sub-mesoscale processes at different stages of eddy development in shaping both eddy function and phytoplankton community structures, highlighting the importance of considering sub-mesoscale physics in the further ecosystem research.</p>