Abstract: Abstract: Due to the seasonal variation of water level in the Three Gorges Reservoir, its surrounding region has turned into a large area of frequent water-fluctuation. The seasonal submergence causes an environment that can lead to difficulty in keeping living for most plants, and thus the serious degradation of vegetation in this area. It is important to screen the flooding-tolerant species for the ecosystem restoration of the water-fluctuation areas in the Three Gorges Reservoir. In this study, we conducted an indoor simulated flooding experiment to study the influences of different flooding stress on the growth and photosynthetic characteristics of mulberry seedlings. One-year seeding of Mulberry was chosen, and three flooding treatments were designed including control with regular irrigation but without submergence, root submergence and deep submergence. The water level in the root submergence treatment was 1 cm higher than soil surface. The depth of water in root and deep submergence was 24 and 60 cm. External morphology of Mulberry were observed during the experiment, the plant height were measured by a measuring tape, the ground diameters were measured by a vernier caliper，and the photosynthetic parameters were measured by Li-cor 6400. The results showed that: 1) The mulberries in the root submergence and deep submergence grew adventitious root, the damage symptoms of mulberries in root submergence group were mild, but the leaves in the deep submergence begun to turn yellow and rot on the 5th day of submergence and barely had leaves in the end; 2) The inhibitory influence of flooding stress on the growth of height and ground diameter of deep-submerged group was far more obvious than the root-all-submerged group; For example, on the 90th day of submergence, the plant height increment of mulberry in the control group, root submergence and deep submergence were 19.5, 14.13 and 2.92 cm, respectively, which was significantly different (P<0.05); 3) The photosynthetic rate, transpiration rate and stomata conductance of mulberries were reduced by the flooding stress; Comparatively, the photosynthetic characteristic values in the root-all-submerged group could remain a higher level, for example, the maximum net photosynthetic rate was up to 65.4% of that in control group; The photosynthesis of mulberry in the deep-submerged group was very weak on the 55th day, when the maximum net photosynthetic rate was only 23.7% of that in the control group, which was significantly different (P<0.05); 4) The photosynthesis characteristic values of the above-water leaves in the deep-submerged group were higher than those of the under-water leaves on the 55th day, suggesting that flooding stress had the large influence on the under-water part of plant than on above-water part; On the 55th day of submergence, the maximum net photosynthetic rate of under-water leaves and above-water leaves in the deep-submerged treatment are 2.53 and 1.14 μmol/(m2·s), respectively, which was significantly different (P<0.05). In conclusion, the one-year mulberry seedlings could not survive for a long time under the deep flooding stress, but they could live well in the root submergence condition. They are more suitable to be planted in high altitudes of water-fluctuation areas of the Three Gorges Reservoir area with low water level during the water storage season. The study could provide data support for selection of plant species in ecological reservation in the Three Gorges Reservoir.