Abstract: To compare the variation patterns of phytoplankton communities and their relationship with environmental factors under the lotus-fish co-culture and conventional pond culture modes, the experiment selected lotus-fish co-culture ponds and conventional culture ponds in Shuangfeng County for comparative research. Through monitoring water quality and phytoplankton in spring, summer, and autumn, the correlations between changes in phytoplankton community structure and water quality factors were analyzed. (1) The concentrations of \rmNO^-_3 -N, TP, TN, and pH in the lotus-fish co-culture group were significantly lower than those in the conventional aquaculture group (P<0.05). (2) A total of 93 phytoplankton species (59 genera in 8 phyla) were identified in the lotus-fish co-culture group, while 71species (50 genera in 7 phyla) were found in the conventional aquaculture group, showing lower species diversity. (3) Significant differences in phytoplankton community structure were observed between the two groups. In the lotus-fish co-culture group, Chlorophyta had the highest density, and Euglenophyta had the highest biomass. In the conventional aquaculture group, Chlorophyta had the highest density in spring and summer, while Cyanophyta dominated in autumn; biomass was primarily composed of Chlorophyta and Bacillariophyta. SIMPER analysis showed that the key algal species causing inter-group differences in spring, summer, and autumn were Navicula, Scenedesmus, and Merismopedia, respectively, all of which were enriched in the conventional aquaculture group. (4) RDA analysis indicated that algal density in the conventional aquaculture group was mainly driven by \rmNO^-_3 -N, TP, and pH, with biomass showing a significant positive correlation with \rmNO^-_3 -N (P<0.05). In the lotus-fish co-culture group, algal density was significantly negatively correlated with \rmNO^-_3 -N, and biomass was mainly regulated by water temperature (P<0.05). Compared with conventional aquaculture, the lotus-fish co-culture model effectively reduce the risk of eutrophication in aquaculture water, promote phytoplankton species diversity, and inhibit cyanobacteria dominance. This study provides a reference for the scientific management of lotus-fish ecological aquaculture.