In order to understand the spatial and temporal distribution characteristics and driving factors of the phytoplankton community in the Lhalu Wetland of Tibet, qualitative and quantitative samples were collected in the main water systems of the wetland in July and October 2021, and May 2022. A total of 126 water samples were collected to explore the species composition and diversity in different seasons and habitats, providing basic data for the study of the ecosystem and sustainable development of the Lhalu Wetland. The results showed that: 1) A total of 532 species of phytoplankton (including varieties and variants) were identified, belonging to 8 phyla, 13 classes, 36 orders, 74 families, and 130 genera, with a species composition of bacillariophyta-chlorophyta-cyanophyta; 2) Significant differences were observed in the characteristics of the phytoplankton community parameters among different seasons and habitats. The Shannon-Wiener diversity index of phytoplankton community in the summer was significantly higher than that in the autumn and spring, while the Simpson dominance index was significantly higher in summer. The Pielou evenness index of phytoplankton community in the autumn was significantly lower than that of the summer and spring. The Margalef richness index of phytoplankton community in the spring was significantly lower than that of the summer and autumn. And that in marsh habitats was significantly higher than that in wet meadow habitats. 4) Season was identified as a key factor influencing the differences in planktonic algae community composition, followed by habitat. The distance decay pattern was more pronounced in summer than that in the autumn and spring. 5) Significant correlations were found between different phytoplankton community parameters and environmental factors in the Lhalu Wetland. 6) Spatial factor made a significant contribution to the variation of the phytoplankton community, while fast-changing water quality variables played a crucial role in determining the seasonal variations of phytoplankton. The explanatory power of season and slow-changing water quality variables was relatively weak but still exerted certain influence on the variation of the phytoplankton community.