Deep high-altitude mountain lakes can act as a natural laboratory, and have the potential to contribute ecological data for understanding the way natural climate and anthropogenic changes that can affect the ecosystems. We present a multi-proxy record from a sediment core from such a lake (Lake Lugu) in southwest China with emphasis on the changes in the testate amoebae community, along with sedimentological data (magnetic susceptibility, total organic carbon/TOC and total nitrogen/TN) over the last 2500 years. In total, 29 testate amoebae species belonging to eight genera (Arcella, Centropyxis, Cyphoderia, Difflugia, Netzelia, Phryganella, Pseudodifflugia and Zivkovicia) were identified. Three stages were clearly defined for the lake based on testate amoebae community. The first stage dated to about 500 BCE–800 CE, with the testate amoebae community dominated by Centropyxis and influenced by soil erosion. The second stage (about 800–1920 CE) was characterized by a gradual increase of TOC and TN and an abrupt shift from Centropyxis-dominated to Difflugia-dominated communities. The third stage (about 1920–2010 CE) showed the pronounced impact of environmental change, high proliferation of Difflugia and a strong influence of human activities. Our results suggest that the testate amoebae assemblages in this high-altitude mountain lake are sensitive paleoenvironmental indicators that can help to monitor alpine lake ecosystem change and model lake succession under changing climate and environment. The potential causes of changes in the testate amoebae species composition and three stages of Lake Lugu succession were soil erosion and pollutants. The soil erosion led to the inwash of terrestrial particles and few testate amoebae species into Lake Lugu showing the importance of stochastic processes. The nutrient enrichment from soil erosion generated disturbances in the environment and species competition that led to the proliferation of some species and disappearance of others through niche based deterministic processes.