The potted adult satsuma mandarin trees were treated under waterlogging stress for 2，5，10，15，and 20 d and normal irrigation was used as the control to observe the changes of its morphological and root anatomical characteristics to study the changes of morphological characteristics and physiological response mechanism of satsuma mandarin （Citrus unshiu Marc.‘Ichifumi Wase’） under waterlogging stress.The photosynthetic parameters of leaves，the osmotic adjustment substances of leaves and roots，the activity of anaerobic respiratory enzymes，the content of malondialdehyde and the mineral nutrients of tree were determined.The results showed that the root system began to have an odor and the phloem cells were full and swollen after 5 days of waterlogging.The new and old leaves had appeared different degrees of yellowing，and the root system began to rot and discolored after 10 days of waterlogging.The tree body withered and died after being submerged for about 20 days.Compared with the control，the activity of alcohol dehydrogenase in the root system was significantly increased at the early stage （within 5 days） of waterlogged stress.The content of free proline，soluble sugar and soluble protein was significantly decreased and maintained at low levels，and the content of malondialdehyde was significantly higher than that of the control only after 10 days of waterlogging.Under the same treatment conditions，the content of chlorophyll in leaves continued to decrease with the waterlogging time.The net photosynthetic rate，stomatal conductance，and transpiration rate of leaves decreased significantly after 10 days of waterlogging，and the concentration of intercellular CO₂ was significantly increased.The content of free proline，soluble protein，malondialdehyde and the relative electrical conductivity in leaves under waterlogging was significantly higher than that of the control at the same period for 10-20 d after waterlogging.Under waterlogging stress for 5 and 20 days，the accumulation of most mineral nutrients in stems and leaves did not change，and the content of P，K，Ca and Mg in root decreased significantly compared with the CK.It is indicated that there are significant differences in the physiological responses of different tissues and organs to waterlogged stress in satsuma aurantium grafted in trifoliate orange rootstock，and the relative electrical conductivity of leaves and the alcohol dehydrogenase in root are sensitive to waterlogged stress.Long-term waterlogging stress affects the photosynthetic performance，the content of osmotic regulation substance and the activity of alcohol dehydrogenase，causing obvious stress symptoms in leaves and roots，resulting in the slow growth and even death of plants.