Abstract: As the primary producer of river ecosystem, the dynamic changes of phytoplankton are related to the stability of fishery resources and water ecosystem. We investigated the community structure of phytoplankton in three typical sections of the Pearl River in dry season (March), wet season (July) and level season (November) in 2021, and evaluated the current situation of water quality by biodiversity and other indicators, so as to provide technical support for the Pearl River water pollution control and water ecological restoration. Results indicate that the species composition, abundance and dominant species of phytoplankton showed significant spatiotemporal changes (P<0.05). A total of 187 species were identified throughout the year (117 in March, 98 in July and 77 in November). The average cell abundance of phytoplankton was 8.6×10⁵, 72.1×10⁵ and 4.0×10⁵ cells·L⁻¹ , and the biomass was 1.235 4, 4.674 5 and 0.569 8 mg·L⁻¹ in March, July and November, respectively. The abundance of Cyanophyta reached 1.18×10⁷ cells·L⁻¹ (Slight cyanobacteria bloom level) in Shijiao section of the Pearl River in wet season. The phytoplankton community structure in the upper reaches of the Pearl River changed from chlorophyta type in dry season to chlorophyta-cyanobacteria type in wet season, and Scenedesmus quadricauda, Merismopedia tenuissima and S. armatus var. boglariensis f. bicaudatus were the dominant species throughout the year. In the lower reaches, the phytoplankton community structure changed from diatomic type to diatom-cyanobacteria type, with Melosira granulata and M. tenuissima as the dominant species. Shannon-Wiener index (H'), Pielou index (J') and Margalef index (D) were 1.58–3.05, 0.51–0.84 and 1.60–3.42, respectively. According to the comprehensive evaluation based on the biodiversity indexes, the water quality in the three typical reaches of the Pearl River was between mild pollution and α-medium pollution, and the water quality still needs to be improved.