The water level fluctuation zone (WLFZ) in the Three Gorges Reservoir is located in the intersection of terrestrial and aquatic ecosystems, and assessing heavy metal pollution in the drown zone is critical for ecological remediation and water conservation. In this study, soils were collected in June and September 2009 in natural recovery area and revegetation area of the WLFZ, and geochemical approaches including geoaccumulation index (I (geo)) and factor analysis and soil microbial community structure were applied to assess the spatial variability and evaluate the influence of revegetation on metals in the WLFZ. Geochemical approaches demonstrated the moderate pollutant of Cd, the slight pollutant of Hg, and four types of pollutant sources including industrial and domestic wastewater, natural rock weathering, traffic exhaust, and crustal materials in the WLFZ. Our results also demonstrated significantly lower concentrations for elements of As, Cd, Pb, Zn, and Mn in the revegetation area. Moreover, soil microbial community structure failed to monitor the heavy metal pollution in such a relatively clean area. Our results suggest that revegetation plays an important role in controlling heavy metal pollution in the WLFZ of the Three Gorges Reservoir, China.