Water and nitrogen (N) are considered the most important factors affecting rice production and play vital roles in regulating soil microbial biomass, activity, and community. The effects of irrigation patterns and N fertilizer levels on the soil microbial community structure and yield of paddy rice were investigated in a pot experiment. The experiment was designed with four N levels of 0 (N0), 126 (N1), 157.5 (N2), and 210 kg N ha-1 (N3) under two irrigation patterns of continuous water-logging irrigation (WLI) and water-controlled irrigation (WCI). Phospholipid fatty acid (PLFA) analysis was conducted to track the dynamics of soil microbial communities at tillering, grain-filling, and maturity stages. The results showed that the maximums of grain yield, above-ground biomass, and total N uptake were all obtained in the N2 treatment under WCI. Similar variations in total PLFAs, as well as bacterial and fungal PLFAs, were found, with an increase from the tillering to the grain-filling stage and a decrease at the maturity stage except for actinomycetic PLFAs, which decreased continuously from the tillering to the maturity stage. A shift in composition of the microbial community at different stages of the plant growth was indicated by principal component analysis (PCA), in which the samples at the vegetative stage (tillering stage) were separated from those at the reproductive stage (grain-filling and maturity stages). Soil microbial biomass, measured as total PLFAs, was significantly higher under WCI than that under WLI mainly at the grain-filling stage, whereas the fungal PLFAs detected under WCI were significantly higher than those under WLI at the tillering, grain-filling, and maturity stages. The application of N fertilizer also significantly increased soil microbial biomass and the main microbial groups both under WLI and WCI conditions. The proper combination of irrigation management and N fertilizer level in this study was the N2 (157.5 kg N ha-1) treatment under the water-controlled irrigation pattern. The effects of irrigation patterns and N fertilizer levels on the soil microbial community structure and yield of paddy rice were investigated in a pot experiment. The experiment was designed with four N levels of 0 (N0), 126 (N1), 157.5 (N2), and 210 kg N ha- 1 (N3) under two irrigation patterns of continuous water-logging irrigation (WLI) and water-controlled irrigation (WCI). Phospholipid fatty acid (PLFA) analysis was conducted to track the dynamics of soil microbial communities at tillering, grain-filling, and maturity stages. The results showed that the maximums of grain yield , above-ground biomass, and total N uptake were all obtained in the N2 treatment under WCI. Similar plots in bacterial and fungal PLFAs, were found, with an increase from the tillering to the grain-filling st age and a decrease at the maturity stage except for actinomycetic PLFAs, which decreased continuously from the tillering to the maturity stage. A shift in composition of the microbial community at different stages of the plant growth was indicated by principal component analysis (PCA), in which the samples at the vegetative stage (tillering stage) were separated from those at the reproductive stage (grain-filling and maturity stages). Soil microbial biomass, measured as total PLFAs, was significantly higher under WCI than that under WLI mainly at the grain -filling stage, while the fungal PLFAs detected under WCI were significantly higher than those under WLI at the tillering, grain-filling, and maturity stages. The application of N fertilizer also significantly increased soil microbial biomass and the main microbial groups both under WLI and WCI conditions. The proper combination of irrigation management and N fertilizer level in this study was the N2 (157.5 kg N ha-1) treatment undefinedr the water-controlled irrigation pattern.