Abstract: The farming of freshwater crayfish Procambarus clarkii in paddy fields is a popular cultivation method, which can account for more than 80% of the annual crayfish production in China. To explore the effects of different fertilization patterns on phytoplankton community structure in paddy fields where P. clarkii were raised, experiments were carried out from April to May 2019 in Taihu Farm in Jingzhou City, Hubei Province. Three kinds of fertilizer, including chemical fertilizer (H), organic fertilizer (Y) and organic-inorganic compound fertilizer (X) were used in different paddy fields. P. clarkii was stocked in each paddy field with a density of 2.30 ind./m². The results showed that 74, 81 and 81 species of phytoplankton were identified in H, Y and X treatments, respectively. The total abundance and total biomass of phytoplankton in H, Y and X treatments ranged from 0.78×10⁶ to 30.32×10⁶ ind./L and 0.55 to 26.00 mg/L, respectively. Both phytoplankton abundance and biomass followed the order H>X>Y. Chlorophyta and Cryptophyta were the most dominant groups, which resulted in the dynamics of phytoplankton community as the fluctuations of these two groups. The Pielou and Shannon-Wiener indexes were higher in Y and X treatments than those in H treatment. In addition, phytoplankton communities showed a more stable state in Y and X treatments than in H treatment. Phytoplankton community in paddy fields exhibited an apparent temporal trend, and water temperature and nutrients were the best drivers for phytoplankton abundance. These results demonstrate that the application of organic-inorganic compound fertilizer in paddy fields can facilitate the growth of phytoplankton and improve the community structure. It is better to apply the compound fertilizer than just one. Since fertilization plays an important role in paddy ecosystem environment, rice and crayfish cultivation, it is of great significance to explore the linkage between fertilization pattern and phytoplankton community in paddy fields.