The composition and functional characteristics of soil microbial community are crucial to the maintenance of ecosystem functions. It is of great significance to identify the structure, community functions and environmental response characteristics of desert soil microbial community for the maintenance of ecosystem stability and diversity protection. In this paper, 16S rRNA and Metagenomics high-throughput sequencing were performed on rhizosphere soil samples of four typical legume shrubs (Caragana spp., Ammopiptanthus mongolicus, Caragana tibetica and Oxytropis aciphylla) from the Baijitan desert steppe in Ningxia. The structure and functional characteristics of the rhizosphere soil bacterial communities and the rhizosphere carbon and nitrogen cycles of the four typical legume shrubs in desert habitats were investigated, and the key environmental factors affecting the microbial communities were also analysed. The results showed that: the richness and diversity of rhizosphere soil bacterial communities were high in the fruit period of the four shrublands, and there was no significant difference among different shrublands. The relative abundances of dominant groups such as Actinobacteria, Proteobacteria and Acidobacteria were different but the differences were not significant. The most dominant bacterial phylum of rhizosphere at different development periods of the four legume shrubs was Actinobacteria (32.98%-44.53%), followed by Proteobacteria, Acidobacteria and Chloroflexi; there were 322 core bacterial genus and the diversity was relatively rich. Arthrobacter, Rubrobacter and Microvirga were the dominant genus that could be defined. Functional annotation of the metagenomics data showed that rhizosphere microbial functional pathways at different development periods of the four legume shrubs differed according to the shrub species and development period. Functional annotations of COG (Cluster of Orthologous Groups of Proteins) and KEGG (Kyoto Encyclopedia of Genes and Genomes) indicated that there were still a large number of unknown functional groups to be explored in the rhizosphere soil of the four shrub species. The functional communities involved in energy generation and conversion, carbohydrate transport metabolism and signal transduction mechanisms were significantly different among the four soils. The abundance of functional groups related to metabolism was the highest at KEGG level 1, accounting for 73.05% on average. Characterisation of the carbon and nitrogen cycles showed that the abundance of genes related to the reduced citrate cycle pathway was higher in carbon fixation and the organic N metabolism pathway was higher in the nitrogen cycle. The rhizosphere soil microorganisms of Caragana spp. had higher gene abundance involved in carbon and nitrogen fixation. Redundancy analysis (RDA) showed that Actinobacteria and Firmicutes were positively correlated with soil total nitrogen (TN), ammonium nitrogen (NH4+-N), total phosphorus (TP) and available phosphorus(AP), Proteobacteria were positively correlated with soil pH, and Acidobacteria were negatively correlated with AP, total potassium (AK) and pH. There was significant positive correlation between carbon fixation pathway and soil nitrogen and phosphorus. NH4+-N, nitrite nitrogen (NO2--N) and TP were positively correlated with nitrogen fixation pathway, and nitrate nitrogen (NO3--N) was positively correlated with organic nitrogen metabolism and denitrification pathway. The results lay a foundation for understanding the diversity of plant rhizosphere soil microorganisms, their genes resources, the environmental response characteristics of soil microbial communities and their adaptation mechanisms in desert steppe habitats.