The change of global precipitation pattern has a great impact on the arid ecosystem. As an indicator of change of soil quality, soil microbes could reflect the material circulation ability, soil fertility, and plant productivity of the ecosystem. Soil microbial biomass carbon (MBC) and nitrogen (MBN) were very sensitive to precipitation changes. The typical desert vegetation on the southeast edge of Tengger Desert was selected as research object in this study. We aimed to provide the scientific basis for further study of microbial carbon and nitrogen and their cycling mechanism in desert ecosystem in the context of global climate change with extreme precipitation events. By using rain shelter and drip systems, five precipitation manipulation treatments were set up, namely extreme drought treatment, moderate drought, contrast, precipitation increasing treatment I, and precipitation increasing treatment II. The response characteristics of desert soil MBC, MBN, and MBC:MBN ratio to different seasons, precipitation and soil depth were studied. The results showed that (1) precipitation manipulation treatments had diverse effects on MBC, MBN, and MBC/MBN ratio. The variation ranges of MBC, MBN, and MBC/MBN ratio were 230.14-272.87 mg/kg, 13.82-17.58 mg/kg, and 19.78-36.06, respectively. Precipitation manipulation treatments had significant effects on MBC and MBN, but not on MBC/MBN ratio. Under extreme drought treatment, the values of MBC and MBN were significantly higher than that of other precipitation treatments. (2) The two-year variation of MBC, MBN, and the ratio of MBC/MBN were significant. Compared with 2016, MBC and MBN significantly decreased and MBC/MBN ratio increased in 2017. (3) MBC, MBN and the ratio of MBC/MBN showed distinct seasonal changes. The range of MBC, MBN, and the ratio of MBC/MBN were 153.31-337.09 mg/kg, 7.89-22.29 mg/kg, and 14.82-46.04, respectively. The highest values of MBC and MBN were in spring, and the lowest values in autumn, while MBC/MBN ratio was the lowest in summer and the highest in winter. (3) The range of MBC, MBN and MBC/MBN ratio in the soil depth of 0-20 cm were 232.57-265.15 mg/kg, 14.00-17.93 mg/kg, and 24.37-32.07, respectively. The MBC and MBN were significant different (P<0.01) among different soil layers, while the values of MBC and MBN in 0-5cm layer were higher than that in both 5-10 cm and 10-20 cm depths. No significant differences of MBC/MBN ratio were found among different soil layers. Therefore, under the global climate background of frequent extreme precipitation events, extreme drought will affect the MBC and MBN in desert ecosystem. Further, it will affect the balance and cycling of carbon and nitrogen, which needs further long-term systematic monitoring.