This essay inquired into the effects of waterlogging and waterlogging recovery treatments on the photosynthetic characteristics and root activity and morphology of the triennial Paeonia ostii. Compared with the control groups (seedlings under normal condition), and thus explored the mechanism of tree peonies in response to waterlogging and recovery. The results revealed that: (1) waterlogging significantly reduced net photosynthetic rate, transpiration rate, stomatal conductance and root activity compared with the control groups. The more waterlogging time, the more reduction. However, the intercellular CO₂ concentration decreased first then increased during the waterlogging. The root activity was the largest decrease in the parameters, only 2.34% of the control groups. The roots are almost black, rotten and even fell off at the waterlogging of 168 h. (2) The decline of photosynthesis was closely related to the regulation of stomatal limitation during the waterlogging of 120 h. However, nonstomatal limitation became the limiting factor of photosynthesis at the waterlogging of 168 h. (3) Net photosynthetic rate, transpiration rate, intercellular CO₂ concentration and root activity of waterlogging recovery groups, went through waterlogging of 72 h, all rose significantly after recovery of 120 h. Net photosynthetic rate and intercellular CO₂ concentration of recovered seedlings increased to the level similar to the control by 168 h. Most of the roots appeared white and relatively developed, and the roots recovered to the normal state. It proves that Paeonia ostii is quick and sensitive to waterlogging. Although subject to waterlogging, it has strong ability of recovery. The research provides theoretical basis for cultivation and management of tree peonies.