Simulation studies on decline phase of Microcystis blooms were carried out in Xiangxi River between 31 July and 28 August, 2009. Relationships between Microcystis cell density (MCD) and environmental parameters were analyzed, and the morphophysiological changes of Microcystis were described in the present research. Results showed that total phosphorus, ammonia-nitrogen, dissolved oxygen, turbidity, conductivity and pH significantly affected the MCD, respectively, but water temperature was negatively correlated (p<0.01) with MCD. During the decline phase, Micro cystis cellular carbohydrate and protein contents decreased, and the large colonies ruptured into small ones which accelerated by raining interference. Meanwhile, most of Microcystis cells were dead, leaving only few living cells. Since water temperature (ranging from 26.4 to 29.3 degrees C) increased gradually and was higher than the suitable growth temperature for Microcystis in the whole experiment, it was concluded that short-term dynamics of Microcystis resulted from changes of multiple environmental parameters rather than the water temperature. Simultaneously, recruitment was considered to contribute little to the formation of Microcystis blooms in Xiangxi River for the remaining living cells which would further decay in the sediment during the over-wintering periods. The present study also demonstrated the convenience of using the in situ enclosures to study the eco-physiological changes of algae.