Abstract: Phytoplankton, as a key and sensitive component of plateau river ecosystems, remains understudied in the middle reaches of the Yarlung Zangbo River regarding its species composition, seasonal dynamics, and particularly the mechanisms of community assembly and their responses to environmental factors. This study employed environmental DNA (eDNA) to systematically analyze the diversity, seasonal dynamics, and driving mechanisms of phytoplankton community in the middle reaches of the Yarlung Zangbo River. A total of 25 sampling sites were established, with water samples collected during both wet and dry seasons. Sequencing results identified six phytoplankton phyla, with Ochrophyta (57.65%) and Chlorophyta (32.42%) being the dominant groups. α-diversity analysis revealed no significant seasonal differences in Simpson and Shannon indices, while the Chao1 index was significantly higher during the dry season than the wet season (P<0.05), indicating seasonal variation in species richness. Significant seasonal variation in community structure was observed (R=0.214, P<0.001), with both geographic and environmental distances exhibiting significant decay effects. Neutral and null models indicated that community assembly was dominated by deterministic processes, with homogenous selection as the primary mechanism. Canonical Correspondence Analysis (CCA) further revealed that water temperature (WT), altitude (ALT), electrical conductivity (EC), chemical oxygen demand (COD) and pH are key environmental factors influencing community structure. This study systematically elucidates the seasonal succession patterns and assembly mechanisms of phytoplankton community in the middle reaches of the Yarlung Zangbo River, providing scientific basis for the conservation of alpine river ecosystems and their response to climate change.