Enclosure is commonly used in the restoration of degraded grasslands. However, the effects of enclosure on grassland plant and soil restoration remain controversial, particularly in deserts. To assess the effects of enclosure on desert plants and soil properties, using high throughput sequencing, the differences between plants and soil were systematically analyzed before and after enclosure construction. The soil organic carbon, total nitrogen and total phosphorus contents of the three desert flora increased and decreased, but the difference was not significant; enclosure increased plant height, coverage, aboveground biomass, and species richness by 58.99%, 59.35%, 33.29%, and 51.21%, respectively, in a Seriphidium transiliense formation; by 15.49%, 33.52%, 20.85%, and 5.13%, respectively, in a Haloxylon persicum formation; and by 83.80%, 31.51%, 76.66% and 33.33%, respectively, in an Anabasis salsa formation. For soil bacteria, enclosure significantly increased the average number of operational taxonomic units and Shannon-Wiener index by 12.74% and 2.92%, respectively, under S. transiliense formation and by 17.08% and 3.17%, respectively, under H. persicum formation. However, enclosure had no significant effect on the average number of operational taxonomic units or Shannon-Wiener index under A. salsa formation. Enclosure significantly increased desert plants, soil bacterial diversity, and desert plant community productivity; however, the increase in soil nutrient content was not significant. These results demonstrate that enclosure is effective for restoring desert ecosystems but may have little effect on the soil nutrient content.