Combined with water quality changes, this paper analysed historical evolution data of phytoplankton, benthic animals, aquatic plants, important composition of ecological systems in Lake Dianchi, and revealed the reasons of degraded ecosystem:the direct cause is disturbances associated with sustained pollutant input, reclaiming land from the lake, building erect breakwater and slow water exchange. Because of Lake Dianchi's geographical location, climate and other reasons, the response of cyanobacterial biomass to nutrient increase is far higher than that of the other lakes(Lake Taihu, Lake Chaohu), which accelerating the shift of macrophytic lake to algal lake; Compared with the ecological system of Lake Taihu and East Lake, Lake Dianchi plateau lake ecosystem is relatively fragile, such as species of sympatric speciation, narrow niche, resulting in poor stability, weak ability of ecosystem recovery. Based on the analysis of ecological pattern, lakeside structure, Lake Dianchi was divided into five ecoregions:heavy pollution region in Lake Caohai, algae accumulation region, aquatic submerged plants protection region, damaged lakeside region and aquatic vegetation damaged region. And then, we proposed a new restoration strategy of ecoregion and step-by-step implementation for the Lake Dianchi, and designed general scheme of the"Southern priority restoration; northern blooming algae and pollution control; western natural protection; eastern periphery breakthrough".