Plant-rhizospheres are known to be hotspots for microbial activities when compared with surrounding bulk soil. The functional importance of rhizosphere microbes had been reported, but information on the function especially under drought remains unclear. Here we analyzed the microbial taxonomy and functions characteristic to rhizosphere soil under different water regimes. In the glasshouse, we grew a desert plant, Encelia farinosa under three water regimes (5%, 8%, and 12%) and analyzed five key enzymes activity, microbial diversity, and functional genes of E. farinosa rhizosphere compared to unplanted soil. The results of plant growth parameters (plant biomass and transpiration) were negatively correlated with that of leucineaminopeptidase activity but positively correlated with acid phosphatase activity. In a comparison of the microbial community structure of E. farinosa, it was different between habitats (rhizosphere and bulk soil) and water regimes, but the variation under different water levels was smaller in the rhizosphere compared to bulk soil. Furthermore, several microbial taxa such as Glomeromycota were varied between bulk and rhizosphere soils. Metagenomic profiling of functional genes abundance scores also indicated differences under drought for bulk soils, but not rhizosphere which may reflect the mediation of drought stress and maintenance of plant-microbes association in rhizosphere soil.