The survival mechanisms of seeds and seedlings of Scirpus mariqueter under the effect of salinity and flooding time were studied to provide an important scientific basis to the ecological restoration of coastal wetlands in the Yangtze Estuary. Different flooding time (8 h/d, h/d 10, 12 h/d, 14 h/d) and salinity (0,5,10,15) were controlled through the simulation of tidal, then the impact of physiological indexes, such as germination rate, germination index, chlorophyll, superoxide dismutase (SOD) and malondialdehyde (MDA) were analyzed. Among them, salinity had the greatest influence on germination rate, germination index and MDA of seedling. Chlorophyll and SOD were mostly influenced in the interaction between salinity and submergence. The results showed that the germination rate reached to the highest when the salinity at 0, and the flooding time at 8 h/d. The critical salinity of the seed germination was 15‰, and the number of turns was the highest at 10‰ and 12 h/d. Chlorophyll was the highest under the interactive treatment of salinity at 0‰ and flooding time of 12 h. What's more, the total activity of SOD was the highest at 10‰ of salinity and 8h/d of flooding time, and MDA was the lowest at 10‰ and 12 h/d. The results showed that the Scirpus mariqueter was most adaptable to moderate salinity (5, 10) and moderate flooding time (10 h/d, 12 h/d).