Abstract: To enhance understanding of phytoplankton communities and water quality in the south-western waters of Xiamen, and to provide foundational data and scientific support for ecological protection, sustainable development and efficient utilization of biological resources, we conducted a field survey at 20 stations in summer, 2022 and investigated the species composition, dominant species, cell density and spatial distribution of diversity of the phytoplankton community. Using statistical methods, we examined the correlation between phytoplankton community structure and environmental factors. As results, a total of 126 phytoplankton species were identified and grouped into 50 genera in 6 phyla. Among these, diatoms had the highest diversity of 106 species in 39 genera, while dinoflagellates had 16 species in 7 genera. Cyanophyta, Euglenophyta, Chlorophyta and Chrysophyta each had one species and genus. The mean phytoplankton cell density was 362.43×10⁴ cells/m³, ranging from 5.22×10⁴cells/m³ to 1 072.54×10⁴cells/m³. High cell density areas were predominantly observed in Jiulong River Estuary and the southern waters of Xiamen. The dominant species included Skeletonema costatum, Pseudo-nitzschia pungens, Asterionella japonica. The average Shannon-Wiener diversity index (H′) and evenness (J) were calculated as 1.74 and 0.35, respectively. Cluster analysis revealed significant differences in community similarity between the western Xiamen waters and other regions. The total number of phytoplankton species remained relatively stable compared to previous surveys. Principal Component Analysis (PCA), redundancy analysis (RDA) and Pearson correlation analysis showed that water temperature, Dissolved Inorganic Nitrogen (DIN) and Chemical Oxygen Demand (COD) is the main environmental factor affecting the phytoplankton community in the south-western waters of Xiamen. The article recommends enhancing the management of eutrophication in Jiulong River runoff for improvements of the marine ecosystem.