The Salix variegata Franch. seedlings planted in the Three Gorges Reservoir (TGR) water level fluctuation zone (WLFZ) could survive after experiencing several seasons of winter submergence. We investigated the recovery mechanisms of S. variegata seedlings planted at the elevation of 168 m and 172 m in the TGR WLFZ after winter submergence. The results indicated that winter submergence caused some impacts on S. variegata seedlings with increases of hydrogen peroxide (H2O2), superoxide anions radical (O₂^-.), and malondialdehyde (MDA) levels, and decreases of antioxidant enzymatic systems during recovery stage after winter submergence. However, further analyses of relative water content (RWC), pigment content, proline content, carbohydrate content and several other antioxidant enzymatic activities (catalase (CAT), guaiacol peroxidase (G-POD), and glutathione peroxidase (GSH-POD)) showed that S. variegata seedlings were well recovered after winter submergence. These results indicate that S. variegata possesses strong winter submergence tolerance and adaptation to the specific hydrological environment in the TGR WLFZ. Therefore, S. variegata should be popularized as native tree species during the revegetation in the TGR WLFZ.