Plants in the water level fluctuation zone of the Three Gorges Reservoir Region disappeared due to winterflooding and prolonged inundation. Revegetation (plantation and natural recovery) have been promoted to restore and protect the riparian ecosystem in recent years. Revegetationmay affect soil qualities and have broad important implications both for ecological services and soil recovery. In this study, we investigated soil properties including soil pH values, bulk density, soil organic matter (SOM), soil nutrients and heavy metals, soil microbial community structure, microbial biomass, and soil quality index under plantation and natural recovery in the Three Gorges Reservoir Region. Most soil properties showed significant temporal and spatial variationsin both the plantation and natural recovery areas. Higher contents of SOM and NO3-N were found in plantation area, while higher contents of soil pH values, bulk density, and totalpotassium were observed in the natural recovery area. However, there were no significant differences in plant richness and diversity and soil microbial community structure betweenthe two restoration approaches. A soil quality index derived from SOM, bulk density, Zn, Cd, and Hg indicated that natural recovery areas with larger herbaceous coverage had more effective capacity for soil restoration.