The objective of this study was to investigate the microbial (bacterial and fungal) community structure and the relationship between community structure and soil chemical properties in the rhizosphere soil of the halophyte Lycium ruthenicum from different geographical locations (habitats), to provide a theoretical basis for further studies on the relationship between rhizosphere microbiomes and the salt tolerance capacity of Lycium ruthenicum. The rhizosphere and bulk soils were collected from the Ebinur Lake wetland of Jinghe county (EB), Wusu city (WS), and Wujiaqu city (WQ). The bacterial 16S rDNA and fungal 18S rDNA were sequenced with Illumina MiSeq high-throughput sequencing, and we analyzed their diversity and community structure. Results showed that the rhizosphere bacterial diversities were higher than those of bulk soils (except for WQ), whereas rhizosphere fungal diversities were lower than those of bulk soils. The bacterial and fungal diversities in bulk soils of WQ were higher than those of EB and WS. The rhizosphere bacterial diversity order was EB > WS > WQ, whereas the rhizosphere fungal diversity was WS > EB > WQ. The most abundant bacterial phyla in rhizosphere soils were Proteobacteria, Bacteroides, Actinomycetes, and Acidobacteria. Ascomycetes and Basidiomycota were the most abundant phyla in the rhizosphere fungal communities. The relative abundances of Proteobacteria, Bacteroidetes, and Acidobacteria in rhizosphere soils were higher than those in bulk soils, whereas that of Firmicutes was the opposite. The differences in relative abundances of dominant fungal phyla between rhizosphere and bulk soils varied among regions. The most abundant rhizosphere bacterial genera were Haliea, Pelagibius, Microbulbifer, Thioprofundum, and Deferrisoma, and genera Melanoleuca, Cochlonema, and Pleospora dominated the rhizosphere fungal communities. The composition and relative abundances of the most-abundant groups (phyla and genera) differed among regions. The relative abundance of Firmicutes in EB was much higher than those in WS and WQ. Most of the halophilic bacteria, such as Halomonas, Geminicoccu, Pelagibius, Gracilimonas, Salinimicrobium, and Planococcus, had much higher abundances in saline-alkali habitat (EB) than in non-saline-alkali habitat (WQ and WS). Microascus was the most abundant genus in the rhizosphere fungal community of EB, while genus Melanoleuca dominated in the rhizosphere fungal communities of WQ and WS. Additionally, the abundances of Geopora, Xenobotrytis, Brachyconidiellopsis, and Pleospora in the rhizosphere soil of EB were much higher than those of WQ and WS. The rhizosphere microbial communities were distinctly separated from the non-rhizosphere communities. The rhizosphere soil microbial communities in all three regions had high similarity to one another, and the same was true for non-rhizosphere communities. The similarity of the microbial communities of non-saline-alkali habitats (WS and WQ) was higher than that of non-saline-alkali and saline-alkali habitats (EB), indicating that soil electrical conductivity had important influences on microbial community composition and abundance.