Desertification and salt stress are major causes of terrestrial ecosystem loss worldwide, and the Gobi, representing a salt-stressed area in inland China, has a major impact on the ecosystems and biodiversity of its surrounding environment. The restoration of the Gobi Desert is an important way to control its expansion, but there are few studies on the evaluation of restoration. In this study, soils under different restoration scenarios, namely, soils in restored areas (R1, R2), semi-restored areas (SR1, SR2), and unrestored control areas (C1, C2), were used to investigate differences in microbial diversity and physicochemical properties. The results showed that the soil was mainly dominated by particles of 4–63 μm (26.45–37.94%) and >63 μm (57.95–72.87%). Across the different restoration levels, the soil pH (7.96–8.43) remained basically unchanged, salinity decreased from 9.23–2.26 to 0.24–0.25, and water content remained constant (10.98–12.27%) except for one restored sample in which it was higher (22.32%). The effective Al, Cu, and Zn in the soil increased, but only slightly. Total organic matter (TOM) decreased from 3.86–5.20% to 1.31–1.47%, and total organic nitrogen (TON) decreased from 0.03–0.06% to 0.01–0.02%, but the difference in total organic carbon (TOC) was not significant. High-throughput testing revealed that the bacterial population of the restored area was dominated by A4b (6.33–9.18%), MND1 (4.94–7.39%), and Vicinamibacteraceae (7.04–7.39%). Regarding archaea, samples from the restored areas were dominated by Marine Group II (76.17–81.49%) and Candidatus Nitrososphaera (6.07–9.75%). PCoA showed that the different restoration levels were the main cause of the differences between the samples. Additionally, salinity was the dominant factor that induced this difference, but it was inhibited by the restoration and targeted enrichment of some of these functional genera. Desert restoration should therefore focus on conserving water rather than adding nutrients. Planting salt- and drought-tolerant vegetation will contribute to the initial restoration of the desert and the restoration of the microbiological content of the soil as it migrates over time, creating a cycle of elements. Restoration stimulates and enhances the microbial diversity of the soil via beneficial microorganisms.
