Abstract: To understand the spatial and temporal dynamics of periphytic algae colony structure and its relationship with environmental factors in the lower reaches of Lhasa River in Tibet Autonomous Region, artificial matrix method was used to investigate the Periphytic algae community structure in the lower reaches of Lhasa River in February (dry season), June (normal season) and September (wet season). Results showed that 104 species belonging to 53 genera and 7 phyla of periplexus were identified, 28 species belonging to diatoms with dominance≥0.02. The first three dominant species were Synedra ulna, Diatom aelongatum and Fragilaria intermedia. The average annual biomass was 0.047 mg/cm², and the highest was found in Qushui County (0.121 mg/cm²), followed by Nimajiangre Township (0.052 mg/cm²) and Lhasa City (0.04 mg/cm²), and the lowest was found in Mozhugongka County (0.015 mg/cm²). The spatial distribution of Periphytic algae biomass in the lower reaches of Lhasa River were Qushui County>Nimajiangre Township>Lhasa City>Alang Township>Zhaxue Township>Dazi County>Mozhugongka county. The temporal distribution of Periphytic algae abundance in the lower reaches of Lhasa River was as follows: normal season>wet season>dry season. The water quality assessment results showed that the water quality of the three sampling points in the upstream was slightly polluted to clean, and the water quality of the four sampling points in the downstream was slightly to moderately over polluted. The canonical correspondence analysis of periphyton community parameters and environmental parameters showed that most dominant species of periphyton were negatively correlated with water temperature, flow rate and pH, and positively correlated with total nitrogen, dissolved oxygen and electrical conductivity. The results of this survey provided the basic data for the conservation and scientific utilization of aquatic biodiversity in Lhasa River basin, Tibet Autonomous Region.