To accurately manage precise feeding and water quality regulation in the rice-duck-crayfish integrated model （RDCI）， continuous monitoring of phytoplankton and physicochemical parameters in the water was conducted from March 2023 to January 2024 in both the RDCI and the rice-crayfish continuous culture model （RCCC）. This study aimed to investigate the community structure characteristics of phytoplankton and their relationships with environmental factors in the RDCI system.The results showed that a total of 214 species from 8 phyla of phytoplankton were found in the RDCI， which is higher than the 196 species from 8 phyla in the RCCC. Both systems were predominantly composed of Chlorophyta， Bacillariophyta， and Euglenophyta. The RDCI had 18 dominant species （Y≥0.02）， more than the 14 in the RCCC. The density of phytoplankton in RDCI ranged from 0.52×10? to 2.19×10? ind/L， with the maximum observed in June and the minimum in April. The biomass ranged from 3.10 to 29.41 mg/L， with the maximum in May and the minimum in July. The annual mean values for the phytoplankton Margalef richness index， Pielou evenness index， and Shannon-Wiener diversity index were 2.45， 0.67， and 1.15， respectively. Compared with RCCC， the density of phytoplankton in RDCI was lower during the crayfish farming and overwintering stages， while the biomass and diversity indices of phytoplankton were higher during the crayfish farming， overwintering， and rice maturity stages.The redundancy analysis results showed that the dominant species of phytoplankton in RDCI were influenced by water temperature， dissolved oxygen， total nitrogen， and total phosphorus. In summary， compared with RCCC， RDCI exhibits higher phytoplankton diversity and better evenness， suggesting a more complex and stable community structure. The species composition of phytoplankton and related indices indicate that RDCI mitigates the degree of eutrophication in water during both the shrimp farming and the overwintering stages， while increasing nutrients levels during the rice planting stage. This approch is benificial for reducing non-point source pollution in agriculture and promoting green agricultural development.