During the period of water storage in the riparian zone of the Three Gorges Reservoir area (TGRA), the nutrients released by decomposing plants will increase the risk of eutrophication. Mowing before flooding is one of the effective ways to reduce the risk of water pollution, but the effect of mowing on the recovery of dominant plants in the riparian zone of the TGRA is not clear. We applied 5 kinds of water treatments including control (CK), shallow flooding (SF), shallow flooding-control (SFK), total flooding (TF), and total flooding-control (TFK) as well as 4 kinds of mowing treatments including no mowing (NC), stubble 30 cm (S30), stubble 20 cm (S20), and stubble 10 cm (S10) to explore the effects of different mowing and flooding treatments on survival, growth and photosynthetic characteristics of C. dactylon. The results showed that: (1) the survival rate of C. dactylon was≥83.3% under different mowing and flooding treatments. (2) Mowing and flooding treatments had significant effects on the morphological growth and biomass allocation of C. dactylon. Compared with the control, the root length, basal diameter and biomass of C. dactylon in SF group were significantly decreased. Likewise, the plant height, basal diameter, root length and biomass of C. dactylon in TF group were significantly decreased. However, in terms of the above-mentioned indicators, SFK and TFK treatments (free from flooding stress) significantly increased compared with SF and TF groups. (3) Mowing and flooding treatments had significant effects on the photosynthetic rate of C. dactylon. The net photosynthetic rate (Pn), stomatal conductance (Gs) and transpiration rate (Ci) of C. dactylon in SF group were significantly decreased; the photosynthesis in TF treatment was not detected because of falling all the leaf. There was no significant difference in photosynthetic rate between SFK group and CK group. The photosynthetic rate of TFK group was higher than that of TF group. (4) Correlation analysis showed that there was a significantly positive correlation between Pn and plant height, root length and biomass of C. dactylon. Comprehensively considering the survival and recovery of C. dactylon, it was found that the optimal mowing treatments were 20 cm and 30 cm of stubble no matter with shallow flooding or total flooding. The results of this study can provide theoretical support for the management of herbaceous vegetation in the riparian zone of TGRA.