In order to explore the characteristics and driving factors of the epilithic algae community in the middle and lower reaches of the Lhasa River, epilithic algae was collected and identified in September 2019, the species composition and spatial distribution were analyzed, and the key environmental factors affecting the epilithic algae community were identified through redundancy analysis. The results indicated that 31 genera of epilithic algae belonging to six phyla were identified, and the average cell density of the epilithic algae was 1.92×106 cells•m-2. The number of species and cell density of the diatom phylum were the largest at each sampling point. The species number and cell density of the epilithic algae were significantly different between the main stream and tributaries. The main stream and tributaries contained relatively small differences in the dominant algae genera, which were Gomphonema, Fragilaria, Cymbella, and Planktolyngbya in the main stream and Gomphonema, Fragilaria, Cymbella, and Oscillatoria in the tributaries. The redundancy analysis revealed that temperature, pH, and dissolved oxygen were the main driving factors affecting the community structure of the dominant genus in the main stream, while HCO3- and flow velocity controlled the community structure of the dominant genus in the tributaries. This study provides basic data and the theoretical basis for the conservation of aquatic ecosystems and water quality management in the middle and lower reaches of the Lhasa River.