Soil microbial communities link soil and plants and play a key role in connecting above-ground and below-ground communities in terrestrial ecosystems. Currently, how artificial revegetation promotes the restoration of soil microbial community diversity in degraded ecosystems attracts extensive attention. In this study, soil samples were collected from long-term artificially restored mobile sandy lands (aerial seeding sample plots) from 1983 to 2015 in the Mu Us Desert. The second-generation high-throughput sequencing technology was adopted to identify soil microorganisms and analyze the changes in their community structure and diversity. The relationships between changes in microbial diversity and soil nutrients were explored by Pearson correlation analysis and canonical correspondence analysis. In addition, the restoration of subsurface soil microbial communities in this area was evaluated. The results are as follows: (1) The alpha diversity of the soil microorganisms increased significantly with the restoration period, and the composition and diversity of the soil microbial communities in the sample plots in different restoration years varied significantly. (2) Soil nutrient indexes, such as total carbon, total nitrogen and nitrate nitrogen, significantly increased with the restoration period and were significantly positively correlated with soil fungal and bacterial diversity. (3) Key soil fungal and bacterial phyla contributed to nutrient cycling in degraded ecosystems. It can be concluded that afforestation by aerial seeding facilitates the change in community structure and increases the diversity of soil microorganisms in the Mu Us Desert. This paper provides a basis for future measures and policies for restoring degraded lands and ecosystems.