Based on water quality monitoring data of Lake Erhai from 1990 to 2013, the yearly and seasonally response characteristics of algal chlorophyll-a to total nitrogen (TN), total phosphorus (TP) and water temperature was investigated using quantile regression method. It indicated that water temperature was always the primary limiting factor of algal biomass indicated by chlorophyll a (Chl-a) across recent 24 years, but its limiting effect on algal Chl-a content was kept descending sharply and replaced much by nutrients (e.g. P, N) with the increasing eutrophic level. Especially the slope values of TP on Chl-a were kept ascending from -0.3 to 0.8. Since 2002, the positive effect of TN on Chl-a presented slow descending tendency, and P became the most important limiting nutrient factor of algal growth. According to the seasonal variation analysis, water temperature and N had dominant effects on algal Chl-a in spring and autumn, but they were replaced by P in the case of Chl-a>8 mg·m~(-3) in spring. In summer, N and P had strong interactive impacts on the algal growth, and the positive effect of P was stronger than that of N in the case of Chl-a>3 mg·m~(-3). In winter, algal biomass was co-limited by temperature and P. It suggested that P reduction is the prior choice of eutrophication control of Lake Erhai, and simultaneously reducing N load is necessary in the background of global warming. In addition,so far a emergency controlling measure should be taken to monitor algal blooming due to sharp ascending of water temperature within a few days in spring and autumn.