Submergence-tolerant trees are essential for vegetation restoration of the hydro-fluctuation zone of the Three Gorges Dam Reservoir (TGDR) area. Thus, it is of great significance to select the submergence-tolerant plant species by conducting in situ studies. To restore degraded riparian vegetation under the circumstances of dynamic impoundment of the TGDR, Salix matsudana Koidz., a flooding-tolerant native tree species, was introduced to conduct an in situ practical study to test its performance in re-vegetating and restoring the hydro-fluctuation zone of the TGDR. Effects of periodic moderate submergence (MS) and deep submergence (DS) on photosynthesis and growth of Salix matsudana Koidz. were investigated after three water cycles compared to a control (i.e., shallow submergence, abbreviated as SS) in order to specifically assess its application prospects in vegetation restoration under such extreme environment. Results showed that net photosynthetic rate (P n ), intrinsic water use efficiency (WUEi) and limiting value of stomata (Ls) of S. matsudana were significantly reduced in DS. However, pigment content had no significant change in all submergence treatments. Diameter at breast height (DBH) and tree height of S. matsudana were significantly decreased in both MS and DS when compared to that of SS, respectively. In contrast, the primary branch number of S. matsudana was significantly increased as submergence increased. In addition, relative diameter and height growth rates of S. matsudana were also reduced under submergence. Considering the sustained growth of this species, S. matsudana saplings are tolerant to long-term periodic submergence and can be applied to the vegetative restoration of the hydro-fluctuation zone of the TGDR region.