Lake environments and ecosystems are known to be sensitive to climate change and human activities. Erhai, a large plateau lake (~250 km²), is characterized by complicated lake morphometry and has experienced multiple environmental stressors (such as eutrophication, water regulation, etc.) over the past few decades. These have led to the deterioration of its water quality and loss of ecosystem resilience, where cyanobacteria blooms have frequently occurred since the 1990s. To uncover the long-term history and spatio-temporal pattern of cyanobacterial blooms in Erhai Lake, multi-proxy analyses of lake sediments from three different parts of the lake basin were conducted and compared. Based on the high-resolution sedimentary pigment data from each core, we found that there existed a strong asynchrony in the long-term changes of algal production among the cores. The significant increase of cyanobacterial pigments in the shallower southern part of the basin started from the late 1980s, earlier than those of the central and northern parts of the lake basin (~1990 and 2000, respectively), with the whole-basin showing cyanobacteria blooms starting from ca. AD 2000. Furthermore, minimum adequate models built to explain the changes in the pigment concentration in the sediments, suggests that climate warming and eutrophication were the main factors that led to the cyanobacteria blooms across the lake basin.In addition, cyanobacteria bloom for the southern part of the lake basin was also related to the water-level fluctuation, hydrodynamics, and macrophyte changes over the last few decades. Overall, our sedimentary records showed that there existed strong heterogeneity in the spatio-temporal patterns of cyanobacterial blooms and the driving factors also varied across space and over the last century in Erhai Lake.. Therefore, taking the current global warming scenario into account, control of both nutrient input and water regulation should be highlighted for ecological restoration and sustainable management of Erhai Lake