Soil water availability is the critical limitation for soil respiration (Rs) and subsequent ecosystem functions in biological soil crusts (BSCs) of arid ecosystems. Thus, uncovering the response mechanism of Rs to different precipitation regimes will improve our knowledge of the potential impacts of global climate change on this fragile ecosystem. To investigate the possible effects of altered precipitation regimes on bacterial community composition, soil properties and soil carbon effluxes, we implemented a 3-year field experiment in a desert shrub in northwestern China with manipulative precipitation treatments consisting of natural precipitation, that increased along a precipitation gradient of 5–40 mm during the growing season. Results showed that microbial biomass carbon and nitrogen (MBC and MBN) were significantly increased with increasing rainfall amount but soil organic carbon, total nitrogen, pH and biological thickness were relatively stable. Water addition significantly altered the bacterial community composition but not its diversity (including richness and evenness) by increasing the relative abundances of Actinobacteria and decreasing those of Bacteroidetes and Cyanobacteria. In addition, MBC was the primary driver that altered bacterial community composition. Soil physiochemical properties resulted in approximately 70% variations in Rs, whereas soil physicochemical properties and bacterial community composition impacted 10% variations in Rs. Our results indicated that bacterial community composition and soil physiochemical properties might be responsible for the responses of Rs to rainfall addition in BSCs of desert regions.