Disentangling the underlying processes of plant adaptations to multiple abiotic stressors is crucial regarding promissory species for the restoration of riparian ecosystems prone to suffering extreme flood and drought events in the context of global climate change and human activities. Distylium chinense is a dominant evergreen shrub, distributed in the riparian areas of the Yangtze River in China. Here, one field study and five controlled experiments (Control, CK; single drought, D; single flooding, FF; from drought to recovery to full flooding, D-R-FF; from full flooding to recovery to drought, FF-R-D) were conducted. More hypertrophied lenticels, adventitious roots, and the increased stem-base hypertrophy of D. chinense were observed under the D-R-FF condition compared with FF and FF-R-D. Interestingly, the increase of the net photosynthetic rate (Pn) coincidentally occurred with the increase of heme degradation by heme oxygenase (r = 0.608, p = 0.003). Pn of D. chinense in D-R-FF was about twice as much as that in FF-R-D. The enhanced photosynthetic performance was functionally coupled with the adequate water supply to promote the tolerance of D. chinense to alternate drought–flooding condition compared with no any flooding condition. The accumulation of soluble sugar was highest under D, followed by FF-R-D, FF and D-R-FF, which showed that soluble sugar accumulation over the drought period could trigger the recovery growth of flooded plants in later flooding. These data provided the first insights into the tolerance mechanisms by a suite of morphological alterations and physiological adaptations, especially in the enhanced photosynthetic performance of D. chinense under alternating drought and flooding stresses. So, D. chinense could be considered as a prominent shrub species in the restoration practices of wetlands, riparian areas, and other flood-prone forests.