In order to reveal the tolerance mechanism of Distylium chinense seedlings to flooding, three treatments were installed, i.e., control (CK), partial flooding (PF) and complete flooding (CF) to simulate the reservoir flooding environments in autumn and winter seasons to study the growth and physiological adaptation mechanisms under different flooding duration and different flooding depth. Flooding significantly affected the biomass of D. chinense seedlings. After treated for 150 days, the biomass of leaf, shoot and root in PF and CF decreased significantly, and the root-shoot ratio also experienced a significant reduction. The content of MDA in PF and CF treatments were not significantly different at the beginning of 90-day flooding, but the content of MDA increased significantly after 120 days of flooding and gradually increased with the rise of flooding depth. The changes of soluble protein in PF and CF were different, while no difference in soluble protein content between CF and CK at the beginning of 60-day flooding. The content of soluble protein in CF increased after 90 days of flooding, while that in PF was not significantly different compared with CK. The content of proline in PF and CF increased at the early of flooding, and dropped to CK level after 90 days of flooding. Similar to MDA, there were no significant changes in the antioxidant enzyme activity (SOD, CAT and APX) at the early of flooding, but flooding caused the antioxidant enzyme activity to increase significantly at the end of flooding. The changes of soluble sugars under each treatment were different. There was no difference in soluble sugars in leaf between PF and CK, while soluble sugars in leaf in CF increased with flooding time gradually decreased. The above results suggest that D. chinense seedlings have high growth and physiological adjustment capability in the flooding environment. This adjustment capability is one of the important reasons for the survival and growth of D. chinense seedlings in hydro-fluctuation belt of the Three Gorges Reservoir region.