Phytoplankton responses to typhoons are pivotal for understanding the impact of climate change on marine biodiversity and productivity, yet current literature, focusing on typhoon-induced biomass increases from nutrient dynamics, might overlook the complexity of plume-upwelling interactions during such events. This study, therefore, examines the sequential impact of Typhoons Bailu and Podul on phytoplankton biomass and community structure in the northern South China Sea, a region where the interplay of riverine discharges and oceanic upwelling shapes the ecological landscape. Employing a combination of in-situ hydrographic measurements, pigment analysis, and satellite data, we tracked the pre- and post-typhoon phytoplankton dynamics, capturing a detailed picture of their response to the rapid hydrodynamic changes induced by these meteorological disturbances. Prior to Typhoon Bailu, a synergetic interaction between the Pearl River plume and coastal upwelling resulted in a diatom-rich phytoplankton assemblage. The passage of Typhoon Bailu followed by Typhoon Podul uncoupled this synergy, leading to phosphate scarcity and a notable decline in overall phytoplankton biomass. This decoupling favored the proliferation of smaller phytoplankton such as Synechococcus and haptophytes_T8, indicating a shift towards a community adapted to phosphate-poor environments. The distinct phytoplankton response patterns observed in this study not only challenge existing paradigms about typhoon impacts on marine productivity but also highlight the complex and potentially transformative effects of typhoon-induced hydrodynamic alterations, although whether the pattern of biomass reduction is generalizable to all similar typhoon events remains uncertain. These insights are essential for modeling the ecological ramifications of such disturbances, which is becoming increasingly important as the frequency and intensity of extreme weather events continue to rise.