Additions of nitrogen (N) and water might have an interactive effect on the structure of the soil microbial community. The effects and importance of a fluctuating natural precipitation regime on the soil microbial community in a semiarid meadow steppe are very variable and less well known. On a S tipa baicalensis R osh. meadow steppe, we used phospholipid fatty acid (PLFA) analysis to evaluate the effects of increased precipitation, addition of nitrogen and precipitation regime in regulating the structure of the microbial community. The experiment had a complete randomized block design with additions of N of 0, 5 and 10 g N m−2 year−1 and of water of 15 or 30% above the natural precipitation from 2010 to 2012. Additional water and number of years had interactive effects on the soil's microbial community structure. The indirect effects of water and N on soil properties such as pH might explain, at least in part, the changes in microbial groups. Additional water significantly decreased PLFAs for most microbial groups in the dry year, but had no effect in the wet year. The results reflected fluctuation in the natural precipitation regime during two hydrologically contrasting years. Changes in the structure of the soil microbial community might depend on variation in interannual precipitation on meadow steppe. Overall, this study emphasizes the importance of the precipitation regime for the soil's microbial community structure. Increases in natural precipitation will weaken the negative effects of nitrogen fertilizers on the grassland ecosystem in future.