Microcystis is one of the most common bloom-forming cyanobacteria in freshwater ecosystems throughout the world. However, the underlying life history mechanism and distinct temporal dynamics (inter- and intra-annual) of Microcystis populations in different geographical locations and lakes remain unclear but is critical information needed for the development of robust prediction, prevention, and management strategies. Perennial observations indicate that temperature may be the key factor driving differences in the overwintering strategy. This study quantitatively compared the overwintering abilities of Microcystis aeruginosa (Ma) in both the water column and sediments under a gradient of overwintering water temperatures (i.e., 4, 8, and 12 & DEG;C) using the death and proliferation rates of Ma. The results show that the dynamics of the Microcystis overwintering strategy were significantly affected by water temperatures. At 4 and 8 & DEG;C, Ma mainly overwintered in sediments and disappeared from the water column after exposure to low temperatures for a long duration, although some Microcystis cells can overwinter in the water column for short durations at low temperatures. At 12 & DEG;C, most Ma can overwinter in the water column. Rising temperatures promoted the proliferation of pelagic Ma but accelerated the death of benthic Ma. With warmer winter temperatures, pelagic Microcystis might become the primary inoculum sources in the spring. Our study highlights the overwintering strategy flexibility in explaining temporal dynamics differences of Microcystis among in geographical locations and should be considered in the context of global warming.