Nitrous oxide (N_2O) is the third-largest contributor to the greenhouse gas emissions driving global climate change. Paddy soil plays a major role in the N_2O emissions. Understanding the microbial regulation mechanism of N_2O production and emission of paddy soil can provide useful information for the study of microbial ecology of soil nitrogen cycle and relieving N_2O emission. Nitrification and denitrification are the two key microbial processes to regulate N_2O emission of rice paddy soil. Here, in our researches within the past ten years, we investigated the characteristics of N_2O emission and microbial regulation mechanism in flooding-drying and fertilization processes based on rice rhizosphere, soil depth and substrate concentration. Meanwhile, the strategy for developing new microorganisms resources and enhancing the N_2O consumption ability was put forward. The method of deep application and reducing fertilizer application in rice field based on decreasing area-source pollution of nitrogen and phosphorus in paddy soil was established, and demonstration and extension had been successfully proceeded. In this paper, the main findings of these researches and other related achievements from domestic and foreign studies are summarized. In combination with the molecular biotechnology, we would carry out the further research work with the following: 1) uncovering the relationship between soil microbes, soil productivity and ecological environment; 2) establishing the analysis platform for functional microbes on genome and transcriptomics level; 3) disclosing associating mechanism between microbial distribution and ecological function; 4) understanding the synthetic mechanism of root-soil-microbes and interaction among plant-endophyte-soil microbes; 5) strengthening practical technology research, transferring of fundamental findings into productive force, and ultimately serving for agricultural production and ecological civilization construction.