As an important freshwater resource in the Qinghai-Tibet Plateau, glacial lakes are being immensely affected by global warming. Due to the lack of long-term monitoring data, the processes and driving mechanisms of the water ecology of these glacial lakes in a rapidly changing climate are poorly understood. This study, for the first time, reconstructed changes in water temperature and photosynthetic microbial communities over the past 200 years in Lake Basomtso, a glacial lake on the southeastern Tibetan Plateau. Temperatures were reconstructed using a paleotemperature proxy based on branched glycerol dialkyl glycerol tetraethers (brGDGTs), the cell membrane lipids of some bacteria, and photosynthetic microbial communities were determined by high-throughput DNA sequencing. The reconstructed mean annual air temperature (MAAT) at Lake Basomtso varied between 6.9 and 8.3 °C over the past 200 years, with a rapid warming rate of 0.25 °C /10 yrs after 1950s. Carbon isotope of sediment and n-alkane analyses indicate that ≥95% of the organic matter in Lake Basomtso is derived from a mixture of terrestrial C plants and endogenous organic matter inputs, and the proportion of endogenous organic matter in the sediments has gradually increased since the 1960s. The sedimentary DNA analyses of the sediment core reveal that Chloracea is the most dominant prokaryotic photosynthetic microbial group (84.5%) over the past 200 years. However, the relative abundance of Cyanobacteria has increased from ≤6.8% before the 1960s to 15.5% nowadays, suggesting that warmer temperatures favor the growth of Cyanobacteria in glacial lakes. Among eukaryotic photosynthetic microorganisms, the Chlorophyceae have been gradually replaced by Dinoflagellata and Diatomacae since the 1980s, although the Chlorophyceae still had the highest average relative abundance overall (30-40%). The Pb isotopic composition, together with the total phosphorous concentration, implies that human activity exerted a minimal impact on Lake Basomtso over the past 200 yrs. However, the synchronous fluctuations of total organic carbon (TOC), total nitrogen (TN), and metal elements in sediments suggest that temperature appears to have a strong influence on nutrient input to Lake Basomtso by controlling glacial erosion. Global warming and the concurrent increase in glacial meltwater are two main factors driving changes in nutrient inputs from terrestrial sources which, in turn, increases the lake productivity, and changes microbial community composition. Our findings demonstrate the sensitive response of glacial lake ecology to global warming. It is necessary to strengthen the monitoring and research of glacial lake ecology on the Tibetan plateau, so as to more scientifically and accurately understand the response process and mechanism of the glacial lake ecosystem under global warming.