Through the experiment with rice-duck intergrowth in rice field, the species, number and biomass analysis of the algae and the aquatic animals were made. The result shows that, there were 39 algal genera and 33 aquatic animals’ genera in the water of these test fields, and the highest genera were in the control field. In the four field, waterhead field, control field, 4-duck field and 6-duck field, the highest algal density was taken in the control field, which the number was 6.075×106ind/L, and the difference was significant. The highest algal biomass was in 4 duck field, and the difference wasn’t significant. The quantitative dominant algal genera were Bacillariophyta, Cyanophyta, Chlorophyta, which accounted for 38.96%, 29.45% and 23.58% of the total algal amount, respectively, while the biomass dominant algae genera were Cyanophyta and Euglenophyta, accounting for 48.23% and 26.72% of total biological quality, respectively. In the water of the rice-duck symbiosis paddy, the dominance of Chlorophyta declined, and that of Euglenophyta and Cyanophyta increased. Both the number and biomass of aquatic animals decrease with an order of waterhead field, control field, 4-duck field and 6-duck field, but the difference wasn’t significant. The quantitative dominant aquatic animals’ genus was Protozoa, while the biomass dominant aquatic animals’ genus was Conchostraco. The highest biodiversity index of algae was in the waterhead and the 4-duck field, which the Shannon-Weiner index was both 2.03, and that of aquatic animals was in the 6-duck field, which the Shannon-Weiner index was 1.765. The conclusion was that the nature attribute of ecosystem with rice-duck intergrowth was increased.