Abstract: To investigate the effect of short-term temperature changes on the colonial and single-cell Microcysis forms, physiological responses were determined after it was cultured at 10℃, 25℃, and 35℃. The results demonstrated that a decline in chlorophyll-a and an increase in superoxide dismutase (SOD) and mortality rates were found when Microcystis was cultured at 10℃ when compared to those cultured at 25℃. Significant decreases in chlorophyll-a and F_v/F_m were observed in the Microcystis single-cell form in contrast to the colonial form, while SOD activity significantly increased when Microcystis was inoculated at 10℃. After culturing at 35℃, chlorophyll-a, mortality rate, and SOD levels significantly increased in single-cell Microcystis, however, a significant decrease in chlorophyll-a and mortality rates and a significant increase in catalase activity was found in colonial Microcystis. The results suggested that short-term temperature stress could affect physiological mechanisms in colonial and single-cell Microcystis. However, colonial Microcystis showed more advantages in adapting to short-term temperature stress than the single-cell form.