The Indian summer monsoon (ISM) is an important part of the global monsoon system. In southwestern China, the abnormal variations of the ISM not only cause abrupt changes of the climate and the ecological environment, but also bring huge economic losses to the society. The late Holocene is the most recent period in geological history. Therefore, understanding the history and mechanisms of the ISM and its influence on the regional hydrology during the late Holocene is important and helpful for predicting the future monsoon precipitation changes in southwestern China. Lake Gongka (3529 m above sea level) is an alpine lake with limited influence from human activities in the Hengduan Mountains and the climate in the region is mainly affected by the ISM. Lake Gongka is sensitive to climate change, making it an ideal region for paleoclimatic research. A 204.5-cm-long continuous and high-quality sediment core was drilled from the center of Lake Gongka (GK20B) by using a steel-barreled Livingstone square-rod piston corer in October, 2020. Four samples of terrestrial plant materials and four total organic matter samples from the core were dated by using the AMS-¹⁴C dating method. Based on the analysis of climatic and environmental proxies including XRF-based elements content, loss-on-ignition (LOI), total organic carbon and nitrogen (TOC, TN) contents and organic carbon isotope (δ¹³C_org), we reconstructed the hydrological changes of the watershed since 3300 cal a BP. The sedimentary lithology which was the inter-bedding between peat and lacustrine sediments and the corresponding changes of climatic and environmental proxies revealed the huge fluctuations of the lake water level during the late Holocene. The results showed that the water level of Lake Gongka had been continuously decreasing in volatility during the late Holocene, which possibly reflected the decreasing trend of the ISM intensity. This trend most likely be associated with the decreasing summer solar insolation in the Northern Hemisphere. In addition, the lake level variations also revealed that the intensity of the ISM fluctuated on centennial time scales, which might be related to the influence of air-sea interactions within the earth's climate system.