Climate change has resulted in frequent heavy and prolonged rainfall events that exacerbate waterlogging stress, leading to the death of certain alpineRhododendrontrees. To shed light on the physiological and molecular mechanisms behind waterlogging stress in woodyRhododendrontrees, we conducted a study ofRhododendron delavayi, a well-known alpine flower species. Specifically, we investigated the physiological and molecular changes that occurred in leaves ofR. delavayisubjected to 30 days of waterlogging stress (WS30d), as well as subsequent post-waterlogging recovery period of 10 days (WS30d-R10d). Our findings reveal that waterlogging stress causes a significant reduction in CO2assimilation rate, stomatal conductance, transpiration rate, and maximum photochemical efficiency of PSII (Fv/Fm) in the WS30d leaves, by 91.2%, 95.3%, 93.3%, and 8.4%, respectively, when compared to the control leaves. Furthermore, the chlorophyll a and total chlorophyll content in the WS30d leaves decreased by 13.5% and 16.6%, respectively. Both WS30d and WS30d-R10d leaves exhibited excessive H2O2accumulation, with a corresponding decrease in lignin content in the WS30d-R10d leaves. At the molecular level, purine metabolism, glutathione metabolism, photosynthesis, and photosynthesis-antenna protein pathways were found to be primarily involved in WS30d leaves, whereas phenylpropanoid biosynthesis, fatty acid metabolism, fatty acid biosynthesis, fatty acid elongation, and cutin, suberin, and wax biosynthesis pathways were significantly enriched in WS30d-R10d leaves. Additionally, both WS30d and WS30d-R10d leaves displayed a build-up of sugars. Overall, our integrated transcriptomic, physiological, and metabolomic analysis demonstrated thatR. delavayiis susceptible to waterlogging stress, which causes irreversible detrimental effects on both its physiological and molecular aspects, hence compromising the tree’s ability to fully recover, even under normal growth conditions.