Taking Tamarix ramosissima seedlings in the natural flooding area along lower reaches of Tarim River as objects, we analyzed the growth of seedlings and variation of the population under continuous flooding disturbance, and the photosynthetic dynamic responses of seedlings under different flood intensities. Conclusions were as following: (1) the population density of T. ramosissima seedlings under continuous twice strong flooding disturbance, from March 2013 to July 2014, increased firstly, then decreased and increased lastly, but the seedlings’ crown, height and stem diameter decreased firstly, then increased and decreased. (2) The population density of the seedlings increased firstly and then decreased in monitoring area Ⅲ in which the second flooding disturbance was weaker, but its crown, height and stem diameter decreased firstly and then increased. (3) The leaf relative water content of the seedlings decreased firstly with the second flooding disturbance decreasing and then increased. At the same time, the chlorophyll content, actual photochemical efficiency of photosystem Ⅱ in the light (ΦPSⅡ), photochemical quenching (qP) of the seedlings decreased, the nonphotochemical quenching (NPQ) increased, but the maximal photochemical efficiencies of PSⅡ (Fv/Fm) maintained optimum value. The research means that although the continuous twice strong flooding disturbance could make the population of T. ramosissima seedlings regenerated, it also cause death to a large number of seedlings for flooding. As a result, the population of T. ramosissima seedlings could not form a certain scale. We suggest that we can adopt the strong and weak alternately manner to conduct ecological water conveyance, which can improve the survival rate of seedlings, and make the seedlings to grow stably.