Mountain lakes in Southwest China are sensitive to regional climate change and catchment development, and an increasing number of surface water bodies have experienced water pollution,rapid community succession and the degradation of ecosystem functioning. The documentary records for Cibi Lake, an alpine lake from northwest Yunnan, showed that this lake has experienced pronounced hydrological fluctuations and human activities for the last three centuries. In this study, a 36-cm long sediment core ( 26°10.6'N, 99°56.4'E) was collected from the deep basin of Cibi Lake(26°06'~26°14'N, 99°51'~99°58'E) and the core was extruded at 0.5 cm intervals for the depth above 5 cm with the core depth below 5 cm sectioned at 1 cm intervals. In the laboratory, we conducted the multi-proxy analyses (including sediment dating, element content and grain size components), to reconstruct the history of lake environmental changes for the last three centuries,meanwhile, together with the diatom analysis for revealing the long-term impact of climate change and human activity on community shift. The chronological profile for the sediment core was constructed through measuring ~(210)Pb and ~(137)Cs radio-activities using a Canberra gamma spectrometer with the constant rate of supply model (CRS). According to the CRS results and the earliest documented time points of Cibi Lake, based on the core depth of 18 cm represents 300 years to analyze the sediments. The grain size composition of the sediments revealed the long-term history of hydrological fluctuation, corresponding well to the documented events of hydrologic regulation and reservoir construction. The diatom community was dominated by planktonic taxa prior to ca. 1860, when Cyclostephanos dubius, known for tolerating strong hydrological fluctuation, was predominant. After ca. 1860,this species was slowly replaced by small-sized planktonic species such as Cyclotella ocellata, with Cyclotella comta being sub-dominant from ca. 1990,the benthic taxa(i.e. Fragilaria spp.) generally increased with obvious fluctuations, with the occurence of eutrophic and planktonic species such as Fragilaria crotonensis. Multivariable analyses further showed that both climate warming and nutrient levels were among the key factors in causing the long-term succession of diatom assemblages, independently explaining 27.5% and 21.3% of community variation, respectively. In addition, the increased input of allochthonous materials and a longer water rendition due to damming may have enhanced nutrient level, leading to a significant shift in diatom assemblage since the 1990s. These results show that Cibi Lake has remained a deep-water and oligotrophic lake over the last three centuries and was characterized by stable thermal stratification,which may have modulated the long-term pattern of biological community response to hydrological and climatic changes. Therefore, the sensitivity of biological indicators to hydrological fluctuation and their differences in response to multiple environmental gradients should be evaluated in paleoenvironmental and paleoecological studies for deep lakes. In the context of climate warming, it is also necessary to highlight the important role of catchment development and hydrological regulation in the sustainable management of alpine lakes in Yunnan.