Abstract: This study contains integrated in situ observations from three research cruises (2019–2020), one of which encountered the tropical cyclone Sinlaku. The results show that the depth-integrated phytoplankton abundance and carbon biomass in the open sea was more than eightfold and sixfold, respectively, than those in the shelf. Diatoms were the major contributors in shelf areas. In the open sea, Trichodesmium was dominant, exhibiting abundances more than sixteen times higher than shelf areas and exceeding diatom and dinoflagellate abundances by three to nine orders of magnitude near the surface. In the period affected by tropical cyclone Sinlaku, total phytoplankton abundance and carbon biomass increased markedly compared to non-cyclone conditions, with horizontal and vertical distributions showing significant fluctuations due to the patchy distribution of high-density aggregations. Dinoflagellates were the dominant carbon biomass contributor at the 25 m layer, accounting for 71.13% of total carbon biomass. Species-level analysis of carbon biomass and equivalent spherical diameter confirmed that chain-forming diatoms and large-size dinoflagellates were significant participants in the carbon pool. Statistical and modeling approaches identified salinity and vertical stratification as key environmental drivers of shelf assemblages, while cyclone-induced coupling of temperature and nutrients played a critical role in shaping open-sea phytoplankton.