Glycyrrhiza inflata is mainly distributed in the desert areas of Xinjiang and Gansu. It is the most salt tolerant medicinal Glycyrrhiza, and plays an important role in improving saline alkali soil. The soil microbial community structure of original habitat is an important basis to reveal the influencing factors of population distribution and the restoration mechanism of saline alkali soil of Glycyrrhiza inflata. In this study, the original habitat soil was collected from five main production areas of Glycyrrhiza inflata, the soil physical and chemical indexes were measured, and the microbial community composition and diversity characteristics were studied by high-throughput sequencing technology combined with Spearman, dbRDA and other methods, so as to reveal the characteristics and influencing factors of dominant microbial communities in different distribution areas. The results showed that Aspergillus, Geomyces, Fusarium in the fungal community, and Stenotrophomonas, Marinimicrobium, and Idiomarina in the bacterial community were the dominant soil microbial groups of the wild Glycyrrhiza inflata habitat. There were significant differences in soil fungal diversity and richness in different distribution areas, but there was no significant difference in soil bacterial diversity and richness. The species of fungi and bacteria in some distribution areas were quite different. Among the soil physical and chemical factors, soil water content and total salinity had significant effects on the community distribution and richness of fungi and bacteria. In original habitat water content was significantly negatively correlated with Aspergillus, Fusarium, Alternaria, Penicillium; significantly positively correlated with Marinnimicrobium, Idiomarina, Aliifodinibius and Salegentibacter, and significantly negatively correlated with Streptomyces. In original habitat soil total salt content was significantly positively correlated with Aspergillus, Gymnoascus, Aporospora, and significantly negatively correlated with Fusarium, Inocybe, Scleroderma; total salt content was significantly correlated with six species of Marinimicrobium, Idiomarina, Halomonas, Aliifodinibius, Salinimicrobium, and Salegentibacter. There was a significant positive correlation between bacterial abundance and a significant negative correlation with Streptomyces and Sphingomonas. In addition, the heterogeneity of the spatial distribution of soil fungi and bacteria was also related to the habitat type and geographical environment of wild Glycyrrhiza inflata. Halomonas, Aliifodinibius and Salegentibacter in this study are all halophilic bacteria in the habitat of Glycyrrhiza inflata. The high abundance of halophilic bacteria in the original habitat may be closely related to the salt adaptation and salt tolerance mechanism of Glycyrrhiza inflata. The results provide a theoretical basis for the population restoration of wild Glycyrrhiza inflata and the soil function restoration of saline alkali abandoned farmland.