Abstract: The study of phytoplankton community structure and its reaction to environmental factors, which plays an important role and has realistic significance, provide a scientific basis for the development of water quality and algal facies management measures. However, there is a lack of researches on the characteristics of phytoplankton community in lotus-fish integrated system, which is the same of comprehensive analysis method of the benefit and its ecological cost. To study the phytoplankton community characteristic of ecosystem and its ecological and economic benefits in lotus-fish integrated system in 2019, a traditional water quality survey following by “Water Quality-Guidance on Sampling Techniques” and “Technical Regulation Waterquality Sampling” and an investigation the phytoplankton community structure according to “The Freshwater Algae of China” were conducted, and then analyzed the three systems of ecological footprint with the local production condition. The results showed that (1) A total of 103 species of 7 phyla of phytoplankton were identified, among which, 56 species of green algae, 21 species of Cyanobacteria, 16 species of Diatoms, 3 species of Euglysophyta, 4 species of Cryptosophyta, 2 species of golden algae and 1 species of Xanthophyta. The water quality of the coculture system was in the clean-less pollution type, which was better than that of the fish monoculture and lotus monoculture, and there were seasonal differences in the dominant species. (2) Redundancy analysis demonstrated that water temperature and dissolved oxygen were the main environmental factors affecting the phytoplankton community. (3) The lowest ecological footprint per ten thousand yuan was in the lotus-fish integrated system in Jinggangshan area, which was 4.48 hm², 80.9% of the fish monoculture pattern and 33.2% of the lotus monoculture. This study indicated that the lotus-fish integrated system in Jinggangshan area of Jiangxi Province has high benefit and low ecological load, and is suitable for local promotion.