Abstract: The paper studied the effects of different flooding stress time on the phenotype and physiological characteristics by using "Taiwan red" pitaya variety seedlings. The results showed that after 20 days of flooding stress，the number of lateral roots began to decrease；under flooding stress for 30 to 40 days，there were wrinkle and wilt on the lateral stems of Pitaya，and disease spots appeared on the base of main stems；under flooding stress for 40 to 50 days，the basal parts of main stems began to decay，and the main roots became significantly shorter. Under flooding stress，SOD activity，POD activity，soluble sugar content，soluble protein content and proline content significantly increased，the maximum values were 2.46，4.18，10.01，1.72 and 2.21 folds than that of the control group respectively；the chlorophyll content remained unchanged，and the content of chlorophyll a > chlorophyll b > carotenoid；and the root activity significantly decreased to 33.21% of the control group. Pitaya plants had some adaptive ability to flooding stress，including the accumulation of proline，soluble sugar and soluble protein，the increase of antioxidant enzyme activity and adventitious roots，which may be beneficial to enhancing the tolerance of Pitaya to flooding stress.