Subalpine lakes are important reserves of biodiversity and freshwater resource, and their unique ecosystems are responsive to environmental changes. Yunzhong Lake, a subalpine reservoir located in the Jiugong Mountains (southeast Hubei province), provides important ecosystem services of tourism, water supply, irrigation and electricity generation. However, the lake has suffered environmental degradation (e.g., algal bloom) since 2000, resulting from wastewater input from local tourist hotels. In order to reveal the response of aquatic biota to anthropogenic and climatic disturbances, multi-proxy analysis (element content, particle size and diatom) and 210Pb dating were applied on a 27-cm length core collected from Yunzhong Lake. The results revealed that sedimentary diatom assemblages were co-dominated by planktonic forms (Aulacoseira and Cyclotella) and benthic forms (Achnanthes and Fragilaria). The results of redundancy analysis (RDA) revealed that sedimentary diatom assemblages of Yunzhong Lake were significantly related to sedimentary elements (i.e., Al, Fe and Pb) and temperature. The cluster analysis of diatom assemblages showed that environmental changes in Yunzhong Lake had experienced two major phases. During the early period after the damming between 1958 and 1993, high abundances of the species preferring alkaline water (i.e., Achnanthes minutissima and Fragilaria nanana) and relatively high values in chemical index of alteration (CIA) mainly responded to strong weathering in the catchment. After 1993, climate warming and nutrient enrichment induced by the development of tourism were two main driving forces of the proliferation of mesotrophic and eutrophic species, such as Cyclotella pseudostelligera and Aulacoseira alpigena. This study reconstructed the evolution of the subalpine lake ecosystem under the combined effects of climate change and human activities. The results can provide baseline information for eco-environmental protection of subalpine lakes and the restoration of water quality in the watershed.