Increased attention has been paid to the influence of coal mining subsidence on ecological environment. Restoration of ecosystem in damaged mining area is critical for restoring disturbed environment. The comparing of plant communities and microbial communities in the artificial restoration and natural restoration areas provides an effective method for evaluating the restoration effects. However, such studies are limited in coal mining subsidence restoration areas. Subsidence area in Shendong mining area, located in the semi-arid region of Western China, was restored from 2003 with 5 ecological restoration plant species. In July 2017, the comparison and analysis of plant and microbial communities were conducted at the artificial restoration areas (AR) and the natural remediation areas (NR). The results showed that the artificial ecological restoration in Shendong mining area has achieved some success, but it has not recovered to a similar ecosystem before the destruction. A higher plant species, coverage and bacterial community diversity were observed in AR. However, these features have lower similarity compared with those in NR sites. Potential soil factors, such as pH, moisture content, total carbon content, organic matter, nitrogen and bulk density, have a greater impact on soil bacterial community structure and diversity. In the ecological restoration of the mining area, attention should be paid to the restoration of soil properties in the mining area. This study can provide theoretical guidance for more scientific ecological restoration in the damaged mining area.