Abstract: The resource and environmental problems caused by excessive consumption of water and fertilizer in rice production have recently aroused widespread concern. This study investigated the effects of irrigation modes (conventional irrigation and 25% water-saved irrigation) and different N application rates (conventional high-nitrogen fertilization and 40% nitrogen-reduced fertilization) on microbial and microfauna assemblages at tillering and ripening stages in paddy field. The results showed that compared with conventional irrigation (CF), water-saved irrigation (WS) decreased the soil pH at tillering stage. Soil dissolved organic matter (dissolved organic C and N) and microbial biomass C and N were significantly affected by irrigation, nitrogen fertilizer and their interactions. WS or N-reduced fertilization (LN) decreased the contents of dissolved organic matter; WS increased microbial biomass C but decreased microbial biomass N. Nitrate was significantly higher in WS than CF, while ammonium showed reverse pattern. At tillering stage, the soil microbial biomass from bacteria, fungi, actinomy and protozoa was higher in WS than in CF, but the trend was opposite at ripening stage. There was a significant interation between irrigation and fertilization on soil rotifer numbers and microbialfeeding nematodes. At tillering stage, WS increased the numbers of rotifer and nematode, and also the proportion of bacterial-feeding nematode; LN increased the abundance of rotifer but decreased the abundance of nematode. In summary, soil microbial and microfauna assemblages showed different response to water-saved and nitrogen-reduced agricultural managements, which depended on different crop growth stages, but also the complex interactions of water and nitrogen and between biological groups in food webs.