Pond culture is the primary method for cultivating Chinese mitten crab (Eriocheir sinensis), with phytoplankton significantly influencing their growth. Green algae benefit crab growth by serving as supplementary food, while cyanobacteria, particularly during blooms, hinder it and pose health risks. Environmental changes in nutrient levels, temperature, and light significantly affect phytoplankton communities in ponds, impacting both ecosystem stability and crab growth. However, there is a limited understanding regarding the patterns of phytoplankton changes within adult Chinese mitten crab culture ponds. This study conducted monthly collection and analysis of phytoplankton throughout the culture cycle in typical adult Chinese mitten crab culture ponds, concurrently measuring physical and chemical water parameters to explore the correlation between phytoplankton changes and environmental factors. The results revealed distinct seasonal variations in phytoplankton composition. Chlorophyta and Bacillariophyta, such as Chlorella, Pediastrum, and Cocconeis, predominated in spring, while Chlorophyta and cyanobacteria, such as Volvox, Anabaena, and Microcystis, dominated in summer, and cyanobacteria and Bacillariophyta, such as Microcystis, Dolichospermum, and Cocconeis, prevailed in autumn. Total phytoplankton density consistently increased throughout the culture period. Microcystis constituted the majority of cyanobacteria biomass throughout most months. Although the total phytoplankton biomass fluctuated, cyanobacteria biomass consistently rose each month, reaching a peak of 61.7 mg/L in October. Water temperature and pH emerged as the primary environmental drivers influencing changes in phytoplankton community structure. Cyanobacteria density reached its peak between 18 and 26 °C and at a pH range of 7.5–8.5. These findings highlight the need for environmental regulation and cyanobacteria control in Chinese mitten crab culture ponds, thus promoting the health and sustainability of the Chinese mitten crab culture.