In order to obtain a better understanding of the ecological status and changing characteristics of the marine ecosystem around the Shengsi Islands under human activities and global warming, we collected net and water samples of phytoplankton and analyzed environmental factors in autumn 2020 and spring 2021. A total of 6 phyla, 54 genera, and 105 species were identified, including 68 species and 33 genera of Bacillariophyta, 30 species and 14 genera of Pyrrophyta, 2 species and 2 genera of all Cyanophyta, Chrysophyta and Cryptophyta, and 1 species and 1 genus of Chlorophyta. Skeletonema spp. was dominant in spring and autumn, especially in autumn with dominance at 0.975. The average cell abundance in spring ((7.17±7.78) cells/mL) was significantly lower than that in autumn ((77.23±73.44) cells/mL). The Shannon-Wiener diversity index and the Pielou's evenness index were higher in spring than in autumn. Spearman correlation analysis showed that phytoplankton abundance was significantly positively correlated with water temperature and transparency, but negatively correlated with salinity. Redundancy analysis revealed that phytoplankton community was highly associated with temperature and nutrients. In addition, a total of 4 phyla, 46 genera, and 94 species were identified using the net collection method, with diatoms accounting for the greatest proportion. The average cell abundances in spring and autumn were 838.17×10³ and 19406.43×10³ cells/m³, respectively. Skeletonema spp. remained the dominant species, with dominance higher than that in water-collected samples. However, the diversity and evenness indices in autumn obtained from net-collected samples (0.23 and 0.05, respectively) were lower than those from water samples (0.38 and 0.10, respectively). Compared with the survey data in 1990 and 2007 using net collection method, we found that phytoplankton community around the Shengsi Islands in spring and autumn has undergone significant changes in the past 30 years. The abundance increased significantly, although the proportion of diatom and dinoflagellate species varied nonsignificantly; the warm-water species number increased markedly; the dominance of Skeletonema spp. increased; and the diversity and evenness indices decreased. These long-term changes in phytoplankton may be largely related to the intensification of warming and eutrophication. The concentration of dissolved inorganic nitrogen showed no significant change in spring, but increased significantly in autumn. Dissolved reactive phosphorus concentration decreased significantly in both spring and autumn. Consequently, N/P increased significantly in both spring and autumn. The changing trend of phytoplankton indicated the ecological and environmental changes around the Shengsi Islands under eutrophication and warming.