The rice-duck complex ecosystem, a type of integrated utilization method of paddy fields, is a major complex planting and breeding model of paddy fields in south China, and opens a new way of sustainable development for rice and waterfowl production.This paper discussed the influences of the stocking of ducks in paddy fields on the species，quantities，diversity and biomass of algae. The field experiment was designed including conventional paddy ecosystem (CK) and rice-duck complex ecosystem (RD). The results showed that there were 6 algal phyla, 57 algal genera and 108 species found in all paddy water during sampling periods, and the phyla were Cyanophyta, Chlorophyta, Bacillariophyta, Euglenophyta, Cryptophyta, Pyrrophyta. The difference of the algal numbers in the two treatments was not obvious, but the algal density and biomass in RD was lower than those in CK. As rice growing, the predominant algal biomass in individual increased in paddy water. The predominant algal species during the early periods of rice growth were Merismopedia glanca, Sceaedsmus quadricauda, Euglena viridis, Cryptomonas erosa, but in the late periods (45th day after putting into ducks), the predominant algal species in CK were Closterium acerosum, Cosmarium quadrum, Cosmarium formosulum etc (belong to Chlorophyta phylum), and the predominant algal species in RD were Euglena viridis, Euglena oxyuris, Phacus longicauda etc. (belong to Euglenophyta phylum). Compared with CK, the algal density and biomass in RD decreased significantly within 15 days after putting into ducks; moreover the content of total P increased, and the content of total N and the genus diversity reduced during the late periods of rice growth (45th day after putting into ducks). Correlation analysis between the algae and the environment factors showed that there were positive relationships between the content of total P, Euglenophyta density and the total biomass of algae, and the indexes were 0.697 and 0.625, respectively.