The rice-fish ecological system is one of the classics practices from the traditional Chinese agriculture. The species composition，density，biomass and diversity of phytoplankton in rice-fish ecological system were investigated to reveal its quantitative characteristics and provide theoretical and practical basis for further development and utilization of this classical agricultural technique. The results showed that there were 6 phyla, 38 genera and 93 species in the plots, including Cyanophyta, Chlorophyta, Bacillariophyta, Euglenophyta, Cryptophyta, and Pyrrophyta. Compared to CK, the rice-fish ecological system increased its density and biomass, decreased the predominance of Bacillariophyta and Cyanophyta, and increased the diversity index.