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The response of soil microbes to global warming, especially their response to precipitation, remains poorly known. The Tibetan Plateau is very sensitive to climate change. In particular, the northeastern margin of the Tibetan Plateau is an interesting area to test the response of soil microbial communities to precipitation, as there is a distinct gradient in annual precipitation from east to west. We collected soil samples along a precipitation gradient in arid and semi-arid areas of the northeastern Tibetan Plateau. Phospholipid fatty acid (PLFA) technology was used to analyze the microbial community structure and total microbial biomass. With declining precipitation, bacterial biomass decreased significantly, whereas fungal biomass did not show an obvious trend; this result indicates that bacteria are more sensitive to mean annual precipitation (MAP). Overall, the biomass of Gram-negative (G(-)) bacteria represented up to 82% of the total bacterial biomass. In the high (260-394 mm yr(-1)) MAP areas, bacterial biomass was mainly concentrated at the surface and decreased with increasing soil depth (0-40 cm). In contrast, in the low (36-260 mm yr(-1)) MAP areas, bacterial biomass was mainly concentrated in the deep soils. The mean annual precipitation was strongly correlated with soil microbial community in space, with microbial communities in the 0-10-cm soil depth most affected by precipitation. Groundwater may impact microbial communities in the 20-40-cm soil depth of this arid and semiarid region. The clustering of the microbial communities was significantly grouped according to the MAP gradient, revealing that MAP is a major driving force of microbial communities in this arid and semi-arid area. The decline in MAP led to a shift in the structure of the microbial community and an overall reduction in microbial biomass.