A great number of palaeoclimatic proxies and modern instrumental data have indicated that the climate of Yunnan- Guizhou Plateau has undergone a significant warming during the past hundred years. In this study to reveal the impact of the region climate change on lake ecosystems, physical and chemical proxies in sediment core from the Lake Lugu were examined, including Loss-on-ignition at 550℃(LOI_550℃), the concentrations of pigments, chlorophyll derivatives (CD), total carotenoids (TC), Oscillaxanthin (Osc), Myxanthophyll (Myx), biogenic silicon and C/N values. The correlations of those proxies with climate data of both temperature and precipitation from nearby Lijiang station during 1951-2010 AD were analyzed. The results showed that four pigment contents and two ratios CD/TC and Osc/Myx were sensitive to regional temperature changes. The CD, TC, Osc, Myx, LOI_550℃ and biogenic silica content showed significantly positive correlations with average annual temperature in the last 60 years, while CD, TC, Osc, Myx and C/N had significantly positive correlations with the 5 years moving average precipitations. The result indicated that warming was possibly one of the main factors driving the increasing of primary productivity of the lake, while the effect of precipitation shows a secondary factor in the comparison. Since 1990, all the four pigments and LOI_550℃ increased significantly while C/N ratios decreased, which indicated that the lake primary productivity were enhanced and its contribution to the total organic matter in sediments increased as well. The increasing of Osc and Myx contents and Osc/Myx ratio in the lake sediments reflected the increase of productivity of Cyanophyceae and the proportion of Oscillatoria in Cyanophyceae. The results indicated that the regional climate change over the last 20 years not only led to the increase of lake primary productivity, but also the change of composition of phytoplankton community, in Lake Lugu.