Abstract: Background Artificial shelter forest planting is regarded as a crucial strategy for sand fixation, windbreak, and soil and water conservation. Populus and Elaeagnus angustifolia are more frequently utilized to create plantations in the soil of road protection forests in desertification areas. It is vital to investigate how different planted forests affect soil microbial ecosystems in order to choose appropriate tree species for road protection forests in Jiayuguan area. Methods The rhizosphere soil of 7-year-old Elaeagnus angustifolia, and Populus artificial shelter forest on the north side of the Lianyungang-Khorgos Expressway in this area was chosen as the research object, with soil at the same depth beside the desertified roads in the same area serving as controls. Each biological duplicate soil was randomly partitioned into two sections. The physical and chemical parameters of the soil were assessed in one portion, while the bacterial and fungal populations in the other were identified using 16SrDNA and ITS high-throughput sequencing technologies. The data were examined using SPSS and other tools. Results 1) Elaeagnus angustifolia and Populus plantation soil pH decreased by 2.51% and 3.84%, soil organic matter increased by 40.87% and 33.77%. 2) The soil bacterial OTUs of Elaeagnus angustifolia and Populus plantation increased by 11.01% and 15.14%, respectively, while the fungal OTUs increased by 23.31% and 22.70%, respectively. 3) Bacterial Chao1 index in Elaeagnus angustifolia and Populus plantation soil increased by 20.92% and 13.90% respectively, fungal Chao1 index increased by 23.31% and 22.70%. 4) After artificial shelter forest planting. In bacteria, the abundance of Proteobacteria and Acidobacteria in the soil increased, while Actinobacteria decreased. In fungi, the richness of Ascomycota slightly decreased, Basidiomycota slightly increased, and Zygomycota significantly increased at the phylum classification level. 5) The dominant bacterial genera in artificial forests are Sphingomonas and Gemmatimonadaceae unclassified. The dominant fungal genera are Geopora and Ascomycota_unclassified. 6) The three dominant bacterial genera in the soil are Gaiellales_unclassified, Actinobacteria_unclassified, and others. The fungal genus is mainly Geopora, and some bacterial groups have not been classified. 7) LEfSe analysis indicated that Elaeagnus angustifolia and Populus plantations shared 7 kinds of high-abundance bacteria, with significant differences compared to the control. There was a significant difference in enriched species between the fungal plantation forest and the control. 8) RDA analysis showed that soil bacterial and fungal communities were driven by pH, organic matter and total potassium respectively, and the associations between the dominant bacterial genera and key environmental factors of different vegetation types were significantly different. Conclusions The artificial shelter forest of Elaeagnus angustifolia significantly enhances the diversity of soil microorganisms and the abundance of Proteobacteria. The distribution of its genera is more closely related to pH and organic matter. The artificial shelter forest of Elaeagnus angustifolia has a better effect on soil improvement, and it is the preferred tree species for the highway shelter forest in Jiayuguan area.