To analyze the effects of flooding stress (control, mild waterflooding, waterflooding and waterlogging) on physiology, biochemistry and leaf structure of Chionanthus virginicus seedlings, and to explore their waterlogging tolerance and physiological mechanism, so as to provide theoretical basis for the introduction and cultivation application of C. virginicus, we used two years old seedlings of C. virginicus as materials to determine the changes of physiological indexes and leaf structure characteristic of C. virginicus seedlings under different degrees of flooding and different stress time points. The results showed that: (1) the POD activity of C. virginicus leaves showed a “decline-rise-decline” trend under mild waterflooding and waterlogging, and showed a first decrease and then increase trend under waterlogging. Under each waterlogging treatment, SOD activity increased first and then decreased, while relative conductivity increased, and MDA accumulated in different degrees. Under mild waterlogging, the contents of SS and SP increased first and then decreased. Under waterflooding and waterlogging, the content of SS increased, and the content of SP decreased first and then increased. (2) With the increase of stress degree, the thickness of leaves increased, the thickness of top and lower epidermis decreased, palisade tissue thickness, spongy tissue thickness, CTR and P/S decreased first and then increased, and SR increased first and then decreased. (3) Under waterlogging stress, the chloroplasts were enlarged and rounded, most of them did not stick to the cell wall, the margins degraded, osmophilic grains and starch grains expanded and increased, and the grana lamellae were vacuolized. The intensification of stress resulted in the degradation of nuclei and chloroplasts, the accumulation of starch granules and cell death. (4) Leaf top epidermis thickness had very significantly positive correlation with SOD activity and significantly positive correlation with POD activity. The Palisade tissue thickness had very significantly positive correlation with the contents of MDA and SS, and significantly positive correlation with the content of SP. Leaf thickness had very significantly positive correlation with relative conductivity, MDA, SS and SP contents. The spongy tissue thickness had significantly positive correlation with the relative conductivity and SS content. In conclusion, mild waterflooding and waterflooding had little effect on C. virginicus seedlings. The seedlings could adapt to stress by adjusting physiological indexes and leaf structure, and had certain waterlogging tolerance. Under waterlogging treatment, the physiological indexes and leaf structure of seedlings changed obviously, and the plants died a lot.