In order to deepen the understanding of the tolerance of Excoecaria cochinchinensis, Nerium oleander and Fagraea ceilanica to intermittent flooding and high concentration of ammonia nitrogen, an intermittent flooding cultivation experiment was conducted with six aqueous solutions of ammonia nitrogen concentration (0, 0.5, 7.5, 14.5, 21.5, 28.5 mg/L). After 90 days of continuous test, the morphological and physiological indexes of the three plants were determined, aimed to provide theoretical references for the application of the three plants in rain garden, subsurface flow wetland, intermittent flooded green space and other environments. The results showed that: (1) Compared with the soil culture control, under intermittent flooding, all three plants showed adaptive changes in enhancing oxygen delivery to the roots, such as enlarged stem base lenticels and adventitious root formation, and significantly promoted the height growth of N. oleander. However, the growth rate of E. cochinchinensis and F. ceilanica was slowed down due to the influence of flooding; (2) Under the interaction of intermittent flooding and ammonia nitrogen, the plant height of N. oleander increased with the increase of ammonia nitrogen concentration, while the plant height growth of E. cochinchinensis and F. ceilanica was significantly inhibited after the ammonia nitrogen reaching 14.5 mg/L, and when the ammonia nitrogen was 21.5 mg/L, the leaves of E. cochinchinensis appeared symptoms such as reduced leaf area and green loss; (3) Intermittent flooding had no significant effect on the activities of antioxidant enzymes and the contents of chlorophyll, malondialdehyde (MDA), free proline (Pro) and soluble protein (SP) of the three plants. On the 60th days, the activities of antioxidant enzymes, free proline and soluble protein of the three plants fluctuated to some extent, but on the 90th day, each index had little difference compared with soil culture; (4) Under the interaction of intermittent flooding and ammonia nitrogen, on the 90th day, N. oleander could recover to the normal level even when the ammonia nitrogen was 28.5 mg/L. After the ammonia nitrogen was 14.5 mg/L, E. cochinchinensis and F. ceilanica tended to produce more antioxidant enzymes, MDA and free proline, less soluble protein, with obvious physiological disorders. It could be seen that N. oleander showed active morphological adaptation and strong resistance in the aqueous solution with ammonia nitrogen concentration of 0-28.5 mg/L, and could grow in a certain length of time and intermittent flooding environment. Although E. cochinchinensis and F. ceilanica also showed strong adaptability, the tolerance to ammonia nitrogen was weaker than that of N. oleander, and they only grew well in the range of 0-14.5 mg/L ammonia nitrogen concentration aqueous solution. Therefore, the three plants could be used in the intermittent flooded green space, and N. oleander has strong adaptability to high concentration ammonia nitrogen water environment.