A 155-day enclosure experiment was conducted to evaluate the effects of co-cultured fish species combination (either the combination of grass carp Ctenopharyngodon idellus, gibel carp Carassius gibelio, silver carp Hypophthalmichthys molitrix and bighead carp Aristichthys nobilis or the combination of silver carp and bighead carp) and formulated feed supplement regime (with or without feed supplement) on phytoplankton community in the enclosures with integrated culture of freshwater pearl mussel Hyriopsis cumingii and fishes. Four treatments, including stocking of grass carp, gibel carp, silver carp and bighead carp with formulated feed supplement (GISB-F ), stocking of grass carp, gibel carp, silver carp and bighead carp without formulated feed supplement (GISB-NF), stocking of silver carp and bighead carp with formulated feed supplement (SB-F), stocking of silver carp and bighead carp without formulated feed supplement (SB-NF), were examined. In each enclosure, 20 mussel, 15 grass carp, 5 gibel carp, 5 silver carp and 5 bighead carp were stocked, respectively. Results showed that the phytoplankton biomass ranged from 3.7 × 10⁸ to 6.0 × 10⁸ cell·L^-1 during the experiment. No significant differences were found in the species composition, biomass and biodiversity index of phytoplankton, dominance index of the dominant species, and the ratio of cyanobacteria biomass to phytoplankton biomass between enclosures GISB-F, GISB-NF, SB-F and SB-NF. However, the concentration of chlorophyll a was higher in the enclosures fed formulated feed than in the enclosures without formulated feed supplement. Seasonal dynamics in phytoplankton community was observed. The dominant species of phytoplankton was green algae (Crucigenia and Scenedesmus) at the beginning of the experiment, and changed to blue-green algae (Merismopedia and Microcyslis) at the end of the experiment, suggesting the trend of occurrence of blue-green algae bloom. The factors that significantly influenced the alteration of community structure of phytoplankton included water temperature (T), ammonia (NH₃-N), total nitrogen (TN) and chemical oxygen demand (COD_Mn). This result indicated that the changes of co-cultured species combination and formulated feed supplement could not change the trend that blue-green algal bloom finally occurred in the enclosures since NH₃-N, TN and COD_Mn increased with the progress of the experiment.