The Zhanjiang Bay ecosystem, frequently influenced by typhoons, represents a highly dynamic coastal environment where elucidating phytoplankton responses to extreme disturbances is essential for sustainable management. This study investigated the impacts of Typhoon Prapiroon on phytoplankton community composition and distribution by employing high-throughput sequencing of the 28S rDNA D1–D2 regions. A total of 137 species belonging to 46 genera was identified, with the ten dominant genera collectively contributing more than 85% of the total abundance, exhibiting substantial shifts in community structure following the typhoon. Salinity was identified as the predominant environmental driver shaping phytoplankton distribution, while temporal analyses revealed lagged community responses to post-typhoon conditions. Moreover, biotic interactions among taxa further influenced patterns of community restructuring. These findings enhance the understanding of phytoplankton resilience mechanisms under extreme climatic disturbances. The integration of phytoplankton monitoring into coastal early warning systems is recommended to inform adaptive management strategies and mitigate ecological risks associated with the increasing frequency and intensity of typhoons, thereby supporting the sustainable use and conservation of estuarine and coastal ecosystems.