Abstract: During the summer of 2020, influenced by Indian Ocean warming and the La Niña event, an anomalous anticyclone formed over the northern South China Sea and the western North Pacific, leading to abnormally high sea surface temperatures in the Beibu Gulf. To investigate the impact of these anomalous climatic conditions in the summer of 2020 on the phytoplankton community structure in the coral distribution area of the Beibu Gulf, this study conducted phytoplankton sampling in the coral zone of Weizhou Island, Guangxi, in September 2020 (during the anomalous climatic period) and September 2021 (non-anomalous period), alongside surveys of water quality parameters and nutrient concentrations. A total of 12 phytoplankton samples were collected to analyze phytoplankton abundance, diversity, and community structure characteristics. Differences in phytoplankton composition, water quality parameters, and nutrient levels were compared between the anomalous climatic period and the post-impact period. The results showed that, compared with September 2021, the coral distribution area of Weizhou Island in September 2020 exhibited lower and more variable salinity, along with higher nutrient concentrations in seawater. This was attributed to the equatorial Pacific anomalous easterly winds associated with La Niña, which triggered the northern South China Sea anticyclone by enhancing convective activity over the Maritime Continent. Consequently, excessive rainfall transported terrestrial nutrients from Weizhou Island into the surrounding waters via surface runoff. Additionally, frequent rainfall suppressed the formation of algal blooms, preventing high dominance of specific phytoplankton taxa despite elevated nutrient availability. Furthermore, heavy rainfall and warming induced by the anticyclone reduced phytoplankton abundance and altered community structure by favoring species adapted to salinity fluctuations and high temperatures.