In order to explore phytoplankton community diversity and its driving factors in the lower reaches of the Yarlung Zangbo River, phytoplankton samples were collected at 34 sites in May 2022 (spring), July 2023 (summer) and September 2023 (autumn). Phytoplankton species were identified by microscopy. Environmental factors during the studied period were investigated. Based on the measured data, the phytoplankton community structure was characterized. The diverse phytoplankton community in different seasons and its driving factors were explored. The results showed that: 1) a total of 269 species and varieties of phytoplankton were identified, belonging to 8 phyla, 10 classes, 22 orders, 40 families and 87 genera. The order of cell abundance was spring＞summer＞autumn. the order of species number was autumn＞spring＞summer. The phytoplankton community structure as a whole showed diatom-green algae-cyanobacteria type. Twelve dominant species were selected, all of which were diatoms. 2) Shannon diversity index, Pielou evenness index, Simpson diversity index and Margalef richness index were lowest in summer. The principal coordinate analysis results showed that there were seasonal variations in phytoplankton community composition. By analyzing β diversity and component decomposition of these three seasons, we found that this difference was mainly due to turnover, in particularly in spring. 3) The neutral community model and the corrected random rate showed that the random process dominated the dynamics of phytoplankton communities in the lower reaches of the Yarlung Zangbo River in these three seasons. The variance decomposition analysis showed that the explanation rate of geographic factors (10.13%) was greater than that of environmental factors (7.46%). Latitude and altitude were the main geographic factors affecting the dynamics of phytoplankton communities. Water temperature was the main environmental factor affecting the dynamics of phytoplankton community. 4) The results of cooccurrence network analysis showed that phytoplankton interaction was mainly cooperative. The community structure in autumn was more concise and stable than that in spring and summer.