Abstract: Three water treatments (control, CK; continuous flooding, CF; and periodic flooding, PF) were installed to simulate the soil moisture change of the riparian zone in the Three Gorges Reservoir (TGR) region of China to study the physiological and ecological adaptation mechanisms of the native plant species Pterocarya stenoptera seedlings to the soil moisture change. All the water treatments had significant effects on the photosynthesis, biomass accumulation, and growth of the P. stenoptera seedlings. As compared with those in CK, the seedling’s net photosynthetic rate (P_n) and stomatal conductance (g_s) in treatments CF and PF were significantly lower while the intercellular carbon dioxide concentration  was significantly higher, and the P_n and g_s in CF and PF declined initially followed by a gradual recovery or tended to be stable. With the extension of treatment time, the total biomass and root, stem, and leaf biomass, plant height, and basal diameter in CF and PF all presented an increasing trend. Throughout the experimental period, the total biomass, root and leaf biomass, and plant height in CF and PF and the stem biomass in PF were significantly lower than those in CK, whereas the stem biomass in CF had no significant difference with that in CK, though the basal diameter in CF was significantly higher than that in CK. It was suggested that the P. stenoptera seedlings had the physiological and ecological characteristics of tolerating flooding rather than flooding-drought alteration.