Due to the periodical water level change of the hydro-fluctuation belt in Three Gorges reservoir area, soil of the hydro-fluctuation belt repeatedly experienced the process of flooding-drought. Thus, most of the original plants were difficult to adapt to the new habitat and that lead to seriously damage of the original ecosystems in the hydro-fluctuation belt. This research imitated the regular pattern of soil moisture condition of the hydro-fluctuation belt in Three Gorges reservoir area and investigated the photosynthetic physiological characteristics and ecological adaptation mechanism of Vetiveria zizanioides under alternating flooding-drought stress with four treatments in 30, 60, 90, and 120 d as cycles. Results showed that different alternating flooding-drought stress significantly affected growth and photosynthetic physiological characteristics of Vetiveria zizanioides seedlings. Plant height, net photosynthetic rate, stomatal conductance, and chlorophyll content physiological variables of each group showed different trends with time. Meanwhile, the alternating cycle was greater, the variation was greater. Whatever, each group eventually can gradually restore or stabilize the state, to maintain a high survival rate. Therefore, Vetiveria zizanioides have a good tolerance and adaptability to flooding and drought. It can be chosen as a plant species for ecological construction in Three Gorges reservoir area.