Abstract: In order to explore the regime shift of phytoplankton community structure and its influencing factors in the Honghu Lake, five sampling sites were set up and phytoplankton samples were collected every month from 2010 to 2019. Sequential t-test analysis of regime shifts (STARS) method was used to study the regime shift of cell density of phytoplankton during wet, normal and dry water seasons from 2010 to 2019. The results showed that the cell density of phytoplankton in the Honghu Lake changed in 2016 during all of the three water seasons. In the process of long-term net enclosure aquaculture in the Honghu Lake, excessive nutrient were putted into the lake, resulting in the water eutrophication and the sediment deterioration. In addition, the massive flood in 2016 caused devastating damage to the ecosystem of the Honghu Lake, leading to the algae bloom. As a result, the regime of algae species in the Honghu Lake changed in 2016. The redundancy analysis showed that the main driving factors affecting phytoplankton in the Honghu Lake were different in different patterns. The significant factors affecting the cell density of phytoplankton before the regime shift during the high water period were transparency, water temperature, and pH, while after the regime shift, the factors changed to transparent, water temperature, dissolved oxygen concentration, potassium permanganate index, total nitrogen concentration and ammonia nitrogen concentration. Before the regime shift during the normal water period, the significant factors affecting the cell density of phytoplankton were water temperature, pH, dissolved oxygen concentration, transparency, ammonia nitrogen concentration and potassium permanganate index, while after the regime shift the factors became potassium permanganate index and dissolved oxygen concentration. During the dry season, the significant factors were pH, dissolved oxygen, total nitrogen concentration and potassium permanganate index before the regime shift, and changed to transparent, pH, total phosphorus concentration, potassium permanganate index, total nitrogen concentration and ammonia nitrogen concentration after the regime shift.