Integrated rice-duck farming system (IRDFS), an environmentally friendly eco-agricultural technique, was developed from the Chinese traditional farming method of raising ducks in paddy fields. Many studies have reported that the farming system has positive ecological effects on paddy ecosystems. In order to further understand the effects of rice-duck farming on population dynamics and functional diversity of microbial flora in paddy soil, we conducted a field experiment with four treatments: rice-duck farming, turbid water, clear water, and conventional rice farming in Zengcheng Research and Education Station in 2005. We then investigated changes in soil microbial communities using agar plate bioassays and BIOLOG techniques. The study results showed that under rice-duck farming, the quantities of culturable bacteria, actinomyces, fungi and microbial community of paddy soil increased in the middle-latter stage of rice growth. Compared to conventional rice farming, bacteria, actinomyces and microbial community significantly increased in the heading stage and ripening stage, and fungi significantly increased in the milky and ripening stage. BIOLOG analysis showed that rice-duck farming increased carbon utilization ability and total metabolic activity of soil microbial communities compared to the clear water plot, and significantly improved functional diversity in the heading stage. This study indicated that integrated rice-duck farming systems had positive effects on improvement of quantity, activity and functional diversity of soil microbial community in paddy fields.