We report 1900-year long records of alknone concentration, C38/C37 ratio, and , and a newly-developed alkenone unsaturation index -based temperatures in a sediment core retrieved from Kusai Lake in the northern Qinghai-Tibetan Plateau. The predominance of C37 and C38 alkenones with minor presence of C39 and C40 alkenones, and the absence of C38 methyl alkenones are indicative of alkneones produced by <i>Isochrysis</i>, which is consistent with the results of sedimentary haptophyte DNA analyses. The interval from 400 to 1200 AD is characterized by higher alkenone concentrations and C38/C37 ratios than the other intervals, which can be attributed to the predominant production of <i>Isochrysis</i> during the entire phytoplankton blooms. With the assistance of information on gene abundance, we attributed this phenomenon to drastic ecological changes in Kusai Lake around 1200 AD in response to climatic changes from warm and wet to cold and dry conditions, and resultant decreased riverine inflow but increased nutrient concentration. The -based temperatures with substituting in a equation concluded based on studies on lakes from high latitude areas in Germany are the most reliable reconstructed summer surface water temperatures for Kusai Lake since they are close to the current summer monthly mean temperature of Wudaoliang Meteorological Station, approximately 50 km to the south of Kusai Lake, and exhibit variations that are generally in accordance with those of the 51-year moving average summer temperatures reconstructed from thicknesses of varve light layers in Kusai Lake sediments. Besides, variations showed by this -based summer surface water temperatures are also generally consistent with those showed by reconstructed temperatures in China.