Lakes, being key regulators of atmospheric carbon dioxide (CO2), have not yet been intensively explored in the carbon cycle. This study provides an attempt to investigate how carbon sequestration in mountain lakes responds to seismic activities, extreme climate events and human disturbance. The new data of grain-size end members (EMs), TN contents, C/N, concentrations of algal spores, and P and Mn contents, in addition to previously published data of TOC and Ca contents, Zr/Rb, Rb/Sr, and land-pollen assemblages of a well-dated sediment core from Yileimu Lake, depicted a more detailed history of environmental evolution in the region. A great earthquake happened in southern Altay at ∼ 3500 cal yr BP that triggered extensive landslides around the lake, and then frequent floods eroded the catchment between ∼ 3500 and 2300 cal yr BP, subsequently severe drought events occurred within the period of 2300–1000 cal yr BP, finally agricultural and pastoral activities intensified within the last 1000 yrs. Organic carbon accumulation rate (OCAR) in Yileimu Lake was extremely high (an underestimated value of ∼ 370 g m–2 yr–1) during the earthquake event, in response to the rapid accumulation of landslide materials. Regional comparison revealed that summer temperature was unexpected to have determined the OCAR during both flood and drought events (average 4.07 and 3.64 g m–2 yr–1, respectively), because it dominated the production of land- and aquatic plants. Human activities increased the OCAR prominently (averages 6.26 g m–2 yr–1) via changing sediment production and vegetation planting, which decoupled the OCAR from climate factors. These data imply that carbon sequestration in lakes from mountain areas where temperature adversity stress dominated vegetation growth would have the potential to increase under anthropogenic warming. In addition, seismically induced carbon sequestration in lakes from tectonically active regions cannot be ignored.